From 896c380170fb573f6dd16c419cc6134a869291ad Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sat, 6 Jul 2019 14:47:51 +0200 Subject: [PATCH 01/11] test data: initial commit --- test-data/empty.ctd | 12 ++++ test-data/empty.xml | 25 +++++++ test-data/float.ctd | 47 +++++++++++++ test-data/float.xml | 158 ++++++++++++++++++++++++++++++++++++++++++ test-data/integer.ctd | 47 +++++++++++++ test-data/integer.xml | 158 ++++++++++++++++++++++++++++++++++++++++++ test-data/macros.xml | 31 +++++++++ test-data/select.ctd | 20 ++++++ test-data/select.xml | 134 +++++++++++++++++++++++++++++++++++ test-data/string.ctd | 20 ++++++ test-data/string.xml | 118 +++++++++++++++++++++++++++++++ 11 files changed, 770 insertions(+) create mode 100644 test-data/empty.ctd create mode 100644 test-data/empty.xml create mode 100644 test-data/float.ctd create mode 100644 test-data/float.xml create mode 100644 test-data/integer.ctd create mode 100644 test-data/integer.xml create mode 100644 test-data/macros.xml create mode 100644 test-data/select.ctd create mode 100644 test-data/select.xml create mode 100644 test-data/string.ctd create mode 100644 test-data/string.xml diff --git a/test-data/empty.ctd b/test-data/empty.ctd new file mode 100644 index 00000000..316502e3 --- /dev/null +++ b/test-data/empty.ctd @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff --git a/test-data/empty.xml b/test-data/empty.xml new file mode 100644 index 00000000..07e534e7 --- /dev/null +++ b/test-data/empty.xml @@ -0,0 +1,25 @@ + + + + + String parameter tests + + echo StringTest + macros.xml + + + + + <![CDATA[echo StringTest + +> $param_stdout +]]> + + + + + <![CDATA[String parameter tests. + + +For more information, visit http://docs.are/unavailable.html]]> + diff --git a/test-data/float.ctd b/test-data/float.ctd new file mode 100644 index 00000000..2ab6c54d --- /dev/null +++ b/test-data/float.ctd @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test-data/float.xml b/test-data/float.xml new file mode 100644 index 00000000..f4fa7405 --- /dev/null +++ b/test-data/float.xml @@ -0,0 +1,158 @@ + + + + + Floateger parameter tests + + echo FloatTest + macros.xml + + + + + <![CDATA[echo FloatTest + +#if str($param_param_wodefault_mandatory_unrestricted): + -param_wodefault_mandatory_unrestricted $param_param_wodefault_mandatory_unrestricted +#end if +#if str($param_param_default_mandatory_unrestricted): + -param_default_mandatory_unrestricted $param_param_default_mandatory_unrestricted +#end if +#if str($param_param_wodefault_optional_unrestricted): + -param_wodefault_optional_unrestricted $param_param_wodefault_optional_unrestricted +#end if +#if str($param_param_default_optional_unrestricted): + -param_default_optional_unrestricted $param_param_default_optional_unrestricted +#end if +#if str($param_param_wodefault_mandatory_unrestricted_min): + -param_wodefault_mandatory_unrestricted_min $param_param_wodefault_mandatory_unrestricted_min +#end if +#if str($param_param_default_mandatory_unrestricted_min): + -param_default_mandatory_unrestricted_min $param_param_default_mandatory_unrestricted_min +#end if +#if str($param_param_wodefault_optional_unrestricted_min): + -param_wodefault_optional_unrestricted_min $param_param_wodefault_optional_unrestricted_min +#end if +#if str($param_param_default_optional_unrestricted_min): + -param_default_optional_unrestricted_min $param_param_default_optional_unrestricted_min +#end if +#if str($param_param_wodefault_mandatory_unrestricted_max): + -param_wodefault_mandatory_unrestricted_max $param_param_wodefault_mandatory_unrestricted_max +#end if +#if str($param_param_default_mandatory_unrestricted_max): + -param_default_mandatory_unrestricted_max $param_param_default_mandatory_unrestricted_max +#end if +#if str($param_param_wodefault_optional_unrestricted_max): + -param_wodefault_optional_unrestricted_max $param_param_wodefault_optional_unrestricted_max +#end if +#if str($param_param_default_optional_unrestricted_max): + -param_default_optional_unrestricted_max $param_param_default_optional_unrestricted_max +#end if +#if str($param_param_wodefault_mandatory_unrestricted_minmax): + -param_wodefault_mandatory_unrestricted_minmax $param_param_wodefault_mandatory_unrestricted_minmax +#end if +#if str($param_param_default_mandatory_unrestricted_minmax): + -param_default_mandatory_unrestricted_minmax $param_param_default_mandatory_unrestricted_minmax +#end if +#if str($param_param_wodefault_optional_unrestricted_minmax): + -param_wodefault_optional_unrestricted_minmax $param_param_wodefault_optional_unrestricted_minmax +#end if +#if str($param_param_default_optional_unrestricted_minmax): + -param_default_optional_unrestricted_minmax $param_param_default_optional_unrestricted_minmax +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv): + -param_wodefault_mandatory_unrestricted_adv $adv_opts.param_param_wodefault_mandatory_unrestricted_adv +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv): + -param_default_mandatory_unrestricted_adv $adv_opts.param_param_default_mandatory_unrestricted_adv +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv): + -param_wodefault_optional_unrestricted_adv $adv_opts.param_param_wodefault_optional_unrestricted_adv +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv): + -param_default_optional_unrestricted_adv $adv_opts.param_param_default_optional_unrestricted_adv +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min): + -param_wodefault_mandatory_unrestricted_adv_min $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_min): + -param_default_mandatory_unrestricted_adv_min $adv_opts.param_param_default_mandatory_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_min): + -param_wodefault_optional_unrestricted_adv_min $adv_opts.param_param_wodefault_optional_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_min): + -param_default_optional_unrestricted_adv_min $adv_opts.param_param_default_optional_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max): + -param_wodefault_mandatory_unrestricted_adv_max $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_max): + -param_default_mandatory_unrestricted_adv_max $adv_opts.param_param_default_mandatory_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_max): + -param_wodefault_optional_unrestricted_adv_max $adv_opts.param_param_wodefault_optional_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_max): + -param_default_optional_unrestricted_adv_max $adv_opts.param_param_default_optional_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax): + -param_wodefault_mandatory_unrestricted_adv_minmax $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_minmax): + -param_default_mandatory_unrestricted_adv_minmax $adv_opts.param_param_default_mandatory_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax): + -param_wodefault_optional_unrestricted_adv_minmax $adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_minmax): + -param_default_optional_unrestricted_adv_minmax $adv_opts.param_param_default_optional_unrestricted_adv_minmax +#end if +#end if +> $param_stdout +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + <![CDATA[Floateger parameter tests. + + +For more information, visit http://docs.are/unavailable.html]]> + diff --git a/test-data/integer.ctd b/test-data/integer.ctd new file mode 100644 index 00000000..356b58da --- /dev/null +++ b/test-data/integer.ctd @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test-data/integer.xml b/test-data/integer.xml new file mode 100644 index 00000000..4ae33636 --- /dev/null +++ b/test-data/integer.xml @@ -0,0 +1,158 @@ + + + + + Integer parameter tests + + echo IntTest + macros.xml + + + + + <![CDATA[echo IntTest + +#if str($param_param_wodefault_mandatory_unrestricted): + -param_wodefault_mandatory_unrestricted $param_param_wodefault_mandatory_unrestricted +#end if +#if str($param_param_default_mandatory_unrestricted): + -param_default_mandatory_unrestricted $param_param_default_mandatory_unrestricted +#end if +#if str($param_param_wodefault_optional_unrestricted): + -param_wodefault_optional_unrestricted $param_param_wodefault_optional_unrestricted +#end if +#if str($param_param_default_optional_unrestricted): + -param_default_optional_unrestricted $param_param_default_optional_unrestricted +#end if +#if str($param_param_wodefault_mandatory_unrestricted_min): + -param_wodefault_mandatory_unrestricted_min $param_param_wodefault_mandatory_unrestricted_min +#end if +#if str($param_param_default_mandatory_unrestricted_min): + -param_default_mandatory_unrestricted_min $param_param_default_mandatory_unrestricted_min +#end if +#if str($param_param_wodefault_optional_unrestricted_min): + -param_wodefault_optional_unrestricted_min $param_param_wodefault_optional_unrestricted_min +#end if +#if str($param_param_default_optional_unrestricted_min): + -param_default_optional_unrestricted_min $param_param_default_optional_unrestricted_min +#end if +#if str($param_param_wodefault_mandatory_unrestricted_max): + -param_wodefault_mandatory_unrestricted_max $param_param_wodefault_mandatory_unrestricted_max +#end if +#if str($param_param_default_mandatory_unrestricted_max): + -param_default_mandatory_unrestricted_max $param_param_default_mandatory_unrestricted_max +#end if +#if str($param_param_wodefault_optional_unrestricted_max): + -param_wodefault_optional_unrestricted_max $param_param_wodefault_optional_unrestricted_max +#end if +#if str($param_param_default_optional_unrestricted_max): + -param_default_optional_unrestricted_max $param_param_default_optional_unrestricted_max +#end if +#if str($param_param_wodefault_mandatory_unrestricted_minmax): + -param_wodefault_mandatory_unrestricted_minmax $param_param_wodefault_mandatory_unrestricted_minmax +#end if +#if str($param_param_default_mandatory_unrestricted_minmax): + -param_default_mandatory_unrestricted_minmax $param_param_default_mandatory_unrestricted_minmax +#end if +#if str($param_param_wodefault_optional_unrestricted_minmax): + -param_wodefault_optional_unrestricted_minmax $param_param_wodefault_optional_unrestricted_minmax +#end if +#if str($param_param_default_optional_unrestricted_minmax): + -param_default_optional_unrestricted_minmax $param_param_default_optional_unrestricted_minmax +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv): + -param_wodefault_mandatory_unrestricted_adv $adv_opts.param_param_wodefault_mandatory_unrestricted_adv +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv): + -param_default_mandatory_unrestricted_adv $adv_opts.param_param_default_mandatory_unrestricted_adv +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv): + -param_wodefault_optional_unrestricted_adv $adv_opts.param_param_wodefault_optional_unrestricted_adv +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv): + -param_default_optional_unrestricted_adv $adv_opts.param_param_default_optional_unrestricted_adv +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min): + -param_wodefault_mandatory_unrestricted_adv_min $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_min): + -param_default_mandatory_unrestricted_adv_min $adv_opts.param_param_default_mandatory_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_min): + -param_wodefault_optional_unrestricted_adv_min $adv_opts.param_param_wodefault_optional_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_min): + -param_default_optional_unrestricted_adv_min $adv_opts.param_param_default_optional_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max): + -param_wodefault_mandatory_unrestricted_adv_max $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_max): + -param_default_mandatory_unrestricted_adv_max $adv_opts.param_param_default_mandatory_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_max): + -param_wodefault_optional_unrestricted_adv_max $adv_opts.param_param_wodefault_optional_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_max): + -param_default_optional_unrestricted_adv_max $adv_opts.param_param_default_optional_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax): + -param_wodefault_mandatory_unrestricted_adv_minmax $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_minmax): + -param_default_mandatory_unrestricted_adv_minmax $adv_opts.param_param_default_mandatory_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax): + -param_wodefault_optional_unrestricted_adv_minmax $adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_minmax): + -param_default_optional_unrestricted_adv_minmax $adv_opts.param_param_default_optional_unrestricted_adv_minmax +#end if +#end if +> $param_stdout +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + <![CDATA[Integer parameter tests. + + +For more information, visit http://docs.are/unavailable.html]]> + diff --git a/test-data/macros.xml b/test-data/macros.xml new file mode 100644 index 00000000..82907e42 --- /dev/null +++ b/test-data/macros.xml @@ -0,0 +1,31 @@ + + + + + requirement + + + + + + + + + + + doi:10.1186/1471-2105-9-163 + + + + + + + + + + + + + + + diff --git a/test-data/select.ctd b/test-data/select.ctd new file mode 100644 index 00000000..f141dd12 --- /dev/null +++ b/test-data/select.ctd @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + diff --git a/test-data/select.xml b/test-data/select.xml new file mode 100644 index 00000000..d79bf0f2 --- /dev/null +++ b/test-data/select.xml @@ -0,0 +1,134 @@ + + + + + String parameter tests + + echo SelectTest + macros.xml + + + + + <![CDATA[echo SelectTest + +#if $param_param_wodefault_mandatory_restricted: + -param_wodefault_mandatory_restricted + #if " " in str($param_param_wodefault_mandatory_restricted): + "$param_param_wodefault_mandatory_restricted" + #else + $param_param_wodefault_mandatory_restricted + #end if +#end if +#if $param_param_default_mandatory_restricted: + -param_default_mandatory_restricted + #if " " in str($param_param_default_mandatory_restricted): + "$param_param_default_mandatory_restricted" + #else + $param_param_default_mandatory_restricted + #end if +#end if +#if $param_param_wodefault_optional_restricted: + -param_wodefault_optional_restricted + #if " " in str($param_param_wodefault_optional_restricted): + "$param_param_wodefault_optional_restricted" + #else + $param_param_wodefault_optional_restricted + #end if +#end if +#if $param_param_default_optional_restricted: + -param_default_optional_restricted + #if " " in str($param_param_default_optional_restricted): + "$param_param_default_optional_restricted" + #else + $param_param_default_optional_restricted + #end if +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_param_wodefault_mandatory_restricted_adv: + -param_wodefault_mandatory_restricted_adv + #if " " in str($adv_opts.param_param_wodefault_mandatory_restricted_adv): + "$adv_opts.param_param_wodefault_mandatory_restricted_adv" + #else + $adv_opts.param_param_wodefault_mandatory_restricted_adv + #end if +#end if + #if $adv_opts.param_param_default_mandatory_restricted_adv: + -param_default_mandatory_restricted_adv + #if " " in str($adv_opts.param_param_default_mandatory_restricted_adv): + "$adv_opts.param_param_default_mandatory_restricted_adv" + #else + $adv_opts.param_param_default_mandatory_restricted_adv + #end if +#end if + #if $adv_opts.param_param_wodefault_optional_restricted_adv: + -param_wodefault_optional_restricted_adv + #if " " in str($adv_opts.param_param_wodefault_optional_restricted_adv): + "$adv_opts.param_param_wodefault_optional_restricted_adv" + #else + $adv_opts.param_param_wodefault_optional_restricted_adv + #end if +#end if + #if $adv_opts.param_param_default_optional_restricted_adv: + -param_default_optional_restricted_adv + #if " " in str($adv_opts.param_param_default_optional_restricted_adv): + "$adv_opts.param_param_default_optional_restricted_adv" + #else + $adv_opts.param_param_default_optional_restricted_adv + #end if +#end if +#end if +> $param_stdout +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + <![CDATA[String parameter tests. + + +For more information, visit http://docs.are/unavailable.html]]> + diff --git a/test-data/string.ctd b/test-data/string.ctd new file mode 100644 index 00000000..11517f36 --- /dev/null +++ b/test-data/string.ctd @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + diff --git a/test-data/string.xml b/test-data/string.xml new file mode 100644 index 00000000..67109ad6 --- /dev/null +++ b/test-data/string.xml @@ -0,0 +1,118 @@ + + + + + String parameter tests + + echo StringTest + macros.xml + + + + + <![CDATA[echo StringTest + +#if str($param_param_wodefault_mandatory_unrestricted): + -param_wodefault_mandatory_unrestricted "$param_param_wodefault_mandatory_unrestricted" +#end if +#if str($param_param_default_mandatory_unrestricted): + -param_default_mandatory_unrestricted "$param_param_default_mandatory_unrestricted" +#end if +#if str($param_param_wodefault_optional_unrestricted): + -param_wodefault_optional_unrestricted "$param_param_wodefault_optional_unrestricted" +#end if +#if str($param_param_default_optional_unrestricted): + -param_default_optional_unrestricted "$param_param_default_optional_unrestricted" +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv): + -param_wodefault_mandatory_unrestricted_adv "$adv_opts.param_param_wodefault_mandatory_unrestricted_adv" +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv): + -param_default_mandatory_unrestricted_adv "$adv_opts.param_param_default_mandatory_unrestricted_adv" +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv): + -param_wodefault_optional_unrestricted_adv "$adv_opts.param_param_wodefault_optional_unrestricted_adv" +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv): + -param_default_optional_unrestricted_adv "$adv_opts.param_param_default_optional_unrestricted_adv" +#end if +#end if +> $param_stdout +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + <![CDATA[String parameter tests. + + +For more information, visit http://docs.are/unavailable.html]]> + From dcd6628636e7254df2de6065b563ec58268f3261 Mon Sep 17 00:00:00 2001 From: Tomnl Date: Tue, 9 Jul 2019 16:21:09 +0100 Subject: [PATCH 02/11] add unit tests --- .travis.yml | 41 +++++++ tests/__init__.py | 0 tests/test-data/AccurateMassSearch.ctd | 44 +++++++ tests/test-data/AccurateMassSearch.xml | 144 ++++++++++++++++++++++ tests/test-data/empty.ctd | 12 ++ tests/test-data/empty.xml | 25 ++++ tests/test-data/float.ctd | 47 ++++++++ tests/test-data/float.xml | 158 +++++++++++++++++++++++++ tests/test-data/integer.ctd | 47 ++++++++ tests/test-data/integer.xml | 158 +++++++++++++++++++++++++ tests/test-data/macros.xml | 31 +++++ tests/test-data/select.ctd | 20 ++++ tests/test-data/select.xml | 134 +++++++++++++++++++++ tests/test-data/string.ctd | 20 ++++ tests/test-data/string.xml | 118 ++++++++++++++++++ tests/test_galaxy_cli.py | 64 ++++++++++ 16 files changed, 1063 insertions(+) create mode 100644 .travis.yml create mode 100644 tests/__init__.py create mode 100644 tests/test-data/AccurateMassSearch.ctd create mode 100644 tests/test-data/AccurateMassSearch.xml create mode 100644 tests/test-data/empty.ctd create mode 100644 tests/test-data/empty.xml create mode 100644 tests/test-data/float.ctd create mode 100644 tests/test-data/float.xml create mode 100644 tests/test-data/integer.ctd create mode 100644 tests/test-data/integer.xml create mode 100644 tests/test-data/macros.xml create mode 100644 tests/test-data/select.ctd create mode 100644 tests/test-data/select.xml create mode 100644 tests/test-data/string.ctd create mode 100644 tests/test-data/string.xml create mode 100644 tests/test_galaxy_cli.py diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 00000000..340840cf --- /dev/null +++ b/.travis.yml @@ -0,0 +1,41 @@ +language: python +python: + - "2.7" + +install: + - sudo apt-get update + - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then + wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh; + else + wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; + fi + - bash miniconda.sh -b -p $HOME/miniconda + - export PATH="$HOME/miniconda/bin:$PATH" + - hash -r + - conda config --set always_yes yes --set changeps1 no + - conda update -q conda + - conda info -a + + - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION + - source activate test-environment + - conda config --add channels conda-forge + - conda config --add channels bioconda + - conda config --add channels anaconda + - conda config --add channels workflowconversion + + - git clone https://github.com/WorkflowConversion/CTDopts $HOME/CTDopts + - cd $HOME/CTDopts + - python setup.py install + - conda install -c conda-forge lxml + - conda install -c conda-forge ruamel.yaml + - conda install libxml2 + - cd $TRAVIS_BUILD_DIR + - python setup.py install + + - conda install coverage green codecov + +script: + - python setup.py test + +after_script: +- python -m codecov diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/tests/test-data/AccurateMassSearch.ctd b/tests/test-data/AccurateMassSearch.ctd new file mode 100644 index 00000000..6092d44e --- /dev/null +++ b/tests/test-data/AccurateMassSearch.ctd @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/AccurateMassSearch.xml b/tests/test-data/AccurateMassSearch.xml new file mode 100644 index 00000000..14bff665 --- /dev/null +++ b/tests/test-data/AccurateMassSearch.xml @@ -0,0 +1,144 @@ + + + + + Match MS signals to molecules from a database by mass. + + AccurateMassSearch + macros.xml + + + + + AccurateMassSearch + +#if str($param_in): + -in $param_in +#end if +#if str($param_out): + -out $param_out +#end if +#if str($param_out_annotation): + -out_annotation $param_out_annotation +#end if +#if str($param_positive_adducts): + -positive_adducts $param_positive_adducts +#end if +#if str($param_negative_adducts): + -negative_adducts $param_negative_adducts +#end if +#if str($param_threads): + -threads $param_threads +#end if +-db:mapping + #for token in $param_db_mapping: + $token + #end for +-db:struct + #for token in $param_db_struct: + $token + #end for +#if str($param_algorithm_mass_error_value): + -algorithm:mass_error_value $param_algorithm_mass_error_value +#end if +#if $param_algorithm_mass_error_unit: + -algorithm:mass_error_unit + #if " " in str($param_algorithm_mass_error_unit): + "$param_algorithm_mass_error_unit" + #else + $param_algorithm_mass_error_unit + #end if +#end if +#if $param_algorithm_ionization_mode: + -algorithm:ionization_mode + #if " " in str($param_algorithm_ionization_mode): + "$param_algorithm_ionization_mode" + #else + $param_algorithm_ionization_mode + #end if +#end if +#if $param_algorithm_isotopic_similarity: + -algorithm:isotopic_similarity +#end if +#if $param_algorithm_keep_unidentified_masses: + -algorithm:keep_unidentified_masses +#end if +#if str($param_algorithm_mzTab_exportIsotopeIntensities): + -algorithm:mzTab:exportIsotopeIntensities $param_algorithm_mzTab_exportIsotopeIntensities +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if str($adv_opts.param_log): + -log "$adv_opts.param_log" +#end if + #if str($adv_opts.param_debug): + -debug $adv_opts.param_debug +#end if + #if $adv_opts.param_no_progress: + -no_progress +#end if + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_test: + -test +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Match MS signals to molecules from a database by mass. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html + diff --git a/tests/test-data/empty.ctd b/tests/test-data/empty.ctd new file mode 100644 index 00000000..316502e3 --- /dev/null +++ b/tests/test-data/empty.ctd @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff --git a/tests/test-data/empty.xml b/tests/test-data/empty.xml new file mode 100644 index 00000000..07e534e7 --- /dev/null +++ b/tests/test-data/empty.xml @@ -0,0 +1,25 @@ + + + + + String parameter tests + + echo StringTest + macros.xml + + + + + <![CDATA[echo StringTest + +> $param_stdout +]]> + + + + + <![CDATA[String parameter tests. + + +For more information, visit http://docs.are/unavailable.html]]> + diff --git a/tests/test-data/float.ctd b/tests/test-data/float.ctd new file mode 100644 index 00000000..2ab6c54d --- /dev/null +++ b/tests/test-data/float.ctd @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/float.xml b/tests/test-data/float.xml new file mode 100644 index 00000000..f4fa7405 --- /dev/null +++ b/tests/test-data/float.xml @@ -0,0 +1,158 @@ + + + + + Floateger parameter tests + + echo FloatTest + macros.xml + + + + + <![CDATA[echo FloatTest + +#if str($param_param_wodefault_mandatory_unrestricted): + -param_wodefault_mandatory_unrestricted $param_param_wodefault_mandatory_unrestricted +#end if +#if str($param_param_default_mandatory_unrestricted): + -param_default_mandatory_unrestricted $param_param_default_mandatory_unrestricted +#end if +#if str($param_param_wodefault_optional_unrestricted): + -param_wodefault_optional_unrestricted $param_param_wodefault_optional_unrestricted +#end if +#if str($param_param_default_optional_unrestricted): + -param_default_optional_unrestricted $param_param_default_optional_unrestricted +#end if +#if str($param_param_wodefault_mandatory_unrestricted_min): + -param_wodefault_mandatory_unrestricted_min $param_param_wodefault_mandatory_unrestricted_min +#end if +#if str($param_param_default_mandatory_unrestricted_min): + -param_default_mandatory_unrestricted_min $param_param_default_mandatory_unrestricted_min +#end if +#if str($param_param_wodefault_optional_unrestricted_min): + -param_wodefault_optional_unrestricted_min $param_param_wodefault_optional_unrestricted_min +#end if +#if str($param_param_default_optional_unrestricted_min): + -param_default_optional_unrestricted_min $param_param_default_optional_unrestricted_min +#end if +#if str($param_param_wodefault_mandatory_unrestricted_max): + -param_wodefault_mandatory_unrestricted_max $param_param_wodefault_mandatory_unrestricted_max +#end if +#if str($param_param_default_mandatory_unrestricted_max): + -param_default_mandatory_unrestricted_max $param_param_default_mandatory_unrestricted_max +#end if +#if str($param_param_wodefault_optional_unrestricted_max): + -param_wodefault_optional_unrestricted_max $param_param_wodefault_optional_unrestricted_max +#end if +#if str($param_param_default_optional_unrestricted_max): + -param_default_optional_unrestricted_max $param_param_default_optional_unrestricted_max +#end if +#if str($param_param_wodefault_mandatory_unrestricted_minmax): + -param_wodefault_mandatory_unrestricted_minmax $param_param_wodefault_mandatory_unrestricted_minmax +#end if +#if str($param_param_default_mandatory_unrestricted_minmax): + -param_default_mandatory_unrestricted_minmax $param_param_default_mandatory_unrestricted_minmax +#end if +#if str($param_param_wodefault_optional_unrestricted_minmax): + -param_wodefault_optional_unrestricted_minmax $param_param_wodefault_optional_unrestricted_minmax +#end if +#if str($param_param_default_optional_unrestricted_minmax): + -param_default_optional_unrestricted_minmax $param_param_default_optional_unrestricted_minmax +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv): + -param_wodefault_mandatory_unrestricted_adv $adv_opts.param_param_wodefault_mandatory_unrestricted_adv +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv): + -param_default_mandatory_unrestricted_adv $adv_opts.param_param_default_mandatory_unrestricted_adv +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv): + -param_wodefault_optional_unrestricted_adv $adv_opts.param_param_wodefault_optional_unrestricted_adv +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv): + -param_default_optional_unrestricted_adv $adv_opts.param_param_default_optional_unrestricted_adv +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min): + -param_wodefault_mandatory_unrestricted_adv_min $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_min): + -param_default_mandatory_unrestricted_adv_min $adv_opts.param_param_default_mandatory_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_min): + -param_wodefault_optional_unrestricted_adv_min $adv_opts.param_param_wodefault_optional_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_min): + -param_default_optional_unrestricted_adv_min $adv_opts.param_param_default_optional_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max): + -param_wodefault_mandatory_unrestricted_adv_max $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_max): + -param_default_mandatory_unrestricted_adv_max $adv_opts.param_param_default_mandatory_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_max): + -param_wodefault_optional_unrestricted_adv_max $adv_opts.param_param_wodefault_optional_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_max): + -param_default_optional_unrestricted_adv_max $adv_opts.param_param_default_optional_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax): + -param_wodefault_mandatory_unrestricted_adv_minmax $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_minmax): + -param_default_mandatory_unrestricted_adv_minmax $adv_opts.param_param_default_mandatory_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax): + -param_wodefault_optional_unrestricted_adv_minmax $adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_minmax): + -param_default_optional_unrestricted_adv_minmax $adv_opts.param_param_default_optional_unrestricted_adv_minmax +#end if +#end if +> $param_stdout +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + <![CDATA[Floateger parameter tests. + + +For more information, visit http://docs.are/unavailable.html]]> + diff --git a/tests/test-data/integer.ctd b/tests/test-data/integer.ctd new file mode 100644 index 00000000..356b58da --- /dev/null +++ b/tests/test-data/integer.ctd @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/integer.xml b/tests/test-data/integer.xml new file mode 100644 index 00000000..4ae33636 --- /dev/null +++ b/tests/test-data/integer.xml @@ -0,0 +1,158 @@ + + + + + Integer parameter tests + + echo IntTest + macros.xml + + + + + <![CDATA[echo IntTest + +#if str($param_param_wodefault_mandatory_unrestricted): + -param_wodefault_mandatory_unrestricted $param_param_wodefault_mandatory_unrestricted +#end if +#if str($param_param_default_mandatory_unrestricted): + -param_default_mandatory_unrestricted $param_param_default_mandatory_unrestricted +#end if +#if str($param_param_wodefault_optional_unrestricted): + -param_wodefault_optional_unrestricted $param_param_wodefault_optional_unrestricted +#end if +#if str($param_param_default_optional_unrestricted): + -param_default_optional_unrestricted $param_param_default_optional_unrestricted +#end if +#if str($param_param_wodefault_mandatory_unrestricted_min): + -param_wodefault_mandatory_unrestricted_min $param_param_wodefault_mandatory_unrestricted_min +#end if +#if str($param_param_default_mandatory_unrestricted_min): + -param_default_mandatory_unrestricted_min $param_param_default_mandatory_unrestricted_min +#end if +#if str($param_param_wodefault_optional_unrestricted_min): + -param_wodefault_optional_unrestricted_min $param_param_wodefault_optional_unrestricted_min +#end if +#if str($param_param_default_optional_unrestricted_min): + -param_default_optional_unrestricted_min $param_param_default_optional_unrestricted_min +#end if +#if str($param_param_wodefault_mandatory_unrestricted_max): + -param_wodefault_mandatory_unrestricted_max $param_param_wodefault_mandatory_unrestricted_max +#end if +#if str($param_param_default_mandatory_unrestricted_max): + -param_default_mandatory_unrestricted_max $param_param_default_mandatory_unrestricted_max +#end if +#if str($param_param_wodefault_optional_unrestricted_max): + -param_wodefault_optional_unrestricted_max $param_param_wodefault_optional_unrestricted_max +#end if +#if str($param_param_default_optional_unrestricted_max): + -param_default_optional_unrestricted_max $param_param_default_optional_unrestricted_max +#end if +#if str($param_param_wodefault_mandatory_unrestricted_minmax): + -param_wodefault_mandatory_unrestricted_minmax $param_param_wodefault_mandatory_unrestricted_minmax +#end if +#if str($param_param_default_mandatory_unrestricted_minmax): + -param_default_mandatory_unrestricted_minmax $param_param_default_mandatory_unrestricted_minmax +#end if +#if str($param_param_wodefault_optional_unrestricted_minmax): + -param_wodefault_optional_unrestricted_minmax $param_param_wodefault_optional_unrestricted_minmax +#end if +#if str($param_param_default_optional_unrestricted_minmax): + -param_default_optional_unrestricted_minmax $param_param_default_optional_unrestricted_minmax +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv): + -param_wodefault_mandatory_unrestricted_adv $adv_opts.param_param_wodefault_mandatory_unrestricted_adv +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv): + -param_default_mandatory_unrestricted_adv $adv_opts.param_param_default_mandatory_unrestricted_adv +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv): + -param_wodefault_optional_unrestricted_adv $adv_opts.param_param_wodefault_optional_unrestricted_adv +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv): + -param_default_optional_unrestricted_adv $adv_opts.param_param_default_optional_unrestricted_adv +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min): + -param_wodefault_mandatory_unrestricted_adv_min $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_min): + -param_default_mandatory_unrestricted_adv_min $adv_opts.param_param_default_mandatory_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_min): + -param_wodefault_optional_unrestricted_adv_min $adv_opts.param_param_wodefault_optional_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_min): + -param_default_optional_unrestricted_adv_min $adv_opts.param_param_default_optional_unrestricted_adv_min +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max): + -param_wodefault_mandatory_unrestricted_adv_max $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_max): + -param_default_mandatory_unrestricted_adv_max $adv_opts.param_param_default_mandatory_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_max): + -param_wodefault_optional_unrestricted_adv_max $adv_opts.param_param_wodefault_optional_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_max): + -param_default_optional_unrestricted_adv_max $adv_opts.param_param_default_optional_unrestricted_adv_max +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax): + -param_wodefault_mandatory_unrestricted_adv_minmax $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_minmax): + -param_default_mandatory_unrestricted_adv_minmax $adv_opts.param_param_default_mandatory_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax): + -param_wodefault_optional_unrestricted_adv_minmax $adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_minmax): + -param_default_optional_unrestricted_adv_minmax $adv_opts.param_param_default_optional_unrestricted_adv_minmax +#end if +#end if +> $param_stdout +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + <![CDATA[Integer parameter tests. + + +For more information, visit http://docs.are/unavailable.html]]> + diff --git a/tests/test-data/macros.xml b/tests/test-data/macros.xml new file mode 100644 index 00000000..82907e42 --- /dev/null +++ b/tests/test-data/macros.xml @@ -0,0 +1,31 @@ + + + + + requirement + + + + + + + + + + + doi:10.1186/1471-2105-9-163 + + + + + + + + + + + + + + + diff --git a/tests/test-data/select.ctd b/tests/test-data/select.ctd new file mode 100644 index 00000000..f141dd12 --- /dev/null +++ b/tests/test-data/select.ctd @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/select.xml b/tests/test-data/select.xml new file mode 100644 index 00000000..d79bf0f2 --- /dev/null +++ b/tests/test-data/select.xml @@ -0,0 +1,134 @@ + + + + + String parameter tests + + echo SelectTest + macros.xml + + + + + <![CDATA[echo SelectTest + +#if $param_param_wodefault_mandatory_restricted: + -param_wodefault_mandatory_restricted + #if " " in str($param_param_wodefault_mandatory_restricted): + "$param_param_wodefault_mandatory_restricted" + #else + $param_param_wodefault_mandatory_restricted + #end if +#end if +#if $param_param_default_mandatory_restricted: + -param_default_mandatory_restricted + #if " " in str($param_param_default_mandatory_restricted): + "$param_param_default_mandatory_restricted" + #else + $param_param_default_mandatory_restricted + #end if +#end if +#if $param_param_wodefault_optional_restricted: + -param_wodefault_optional_restricted + #if " " in str($param_param_wodefault_optional_restricted): + "$param_param_wodefault_optional_restricted" + #else + $param_param_wodefault_optional_restricted + #end if +#end if +#if $param_param_default_optional_restricted: + -param_default_optional_restricted + #if " " in str($param_param_default_optional_restricted): + "$param_param_default_optional_restricted" + #else + $param_param_default_optional_restricted + #end if +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_param_wodefault_mandatory_restricted_adv: + -param_wodefault_mandatory_restricted_adv + #if " " in str($adv_opts.param_param_wodefault_mandatory_restricted_adv): + "$adv_opts.param_param_wodefault_mandatory_restricted_adv" + #else + $adv_opts.param_param_wodefault_mandatory_restricted_adv + #end if +#end if + #if $adv_opts.param_param_default_mandatory_restricted_adv: + -param_default_mandatory_restricted_adv + #if " " in str($adv_opts.param_param_default_mandatory_restricted_adv): + "$adv_opts.param_param_default_mandatory_restricted_adv" + #else + $adv_opts.param_param_default_mandatory_restricted_adv + #end if +#end if + #if $adv_opts.param_param_wodefault_optional_restricted_adv: + -param_wodefault_optional_restricted_adv + #if " " in str($adv_opts.param_param_wodefault_optional_restricted_adv): + "$adv_opts.param_param_wodefault_optional_restricted_adv" + #else + $adv_opts.param_param_wodefault_optional_restricted_adv + #end if +#end if + #if $adv_opts.param_param_default_optional_restricted_adv: + -param_default_optional_restricted_adv + #if " " in str($adv_opts.param_param_default_optional_restricted_adv): + "$adv_opts.param_param_default_optional_restricted_adv" + #else + $adv_opts.param_param_default_optional_restricted_adv + #end if +#end if +#end if +> $param_stdout +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + <![CDATA[String parameter tests. + + +For more information, visit http://docs.are/unavailable.html]]> + diff --git a/tests/test-data/string.ctd b/tests/test-data/string.ctd new file mode 100644 index 00000000..11517f36 --- /dev/null +++ b/tests/test-data/string.ctd @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/string.xml b/tests/test-data/string.xml new file mode 100644 index 00000000..67109ad6 --- /dev/null +++ b/tests/test-data/string.xml @@ -0,0 +1,118 @@ + + + + + String parameter tests + + echo StringTest + macros.xml + + + + + <![CDATA[echo StringTest + +#if str($param_param_wodefault_mandatory_unrestricted): + -param_wodefault_mandatory_unrestricted "$param_param_wodefault_mandatory_unrestricted" +#end if +#if str($param_param_default_mandatory_unrestricted): + -param_default_mandatory_unrestricted "$param_param_default_mandatory_unrestricted" +#end if +#if str($param_param_wodefault_optional_unrestricted): + -param_wodefault_optional_unrestricted "$param_param_wodefault_optional_unrestricted" +#end if +#if str($param_param_default_optional_unrestricted): + -param_default_optional_unrestricted "$param_param_default_optional_unrestricted" +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv): + -param_wodefault_mandatory_unrestricted_adv "$adv_opts.param_param_wodefault_mandatory_unrestricted_adv" +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv): + -param_default_mandatory_unrestricted_adv "$adv_opts.param_param_default_mandatory_unrestricted_adv" +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv): + -param_wodefault_optional_unrestricted_adv "$adv_opts.param_param_wodefault_optional_unrestricted_adv" +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv): + -param_default_optional_unrestricted_adv "$adv_opts.param_param_default_optional_unrestricted_adv" +#end if +#end if +> $param_stdout +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + <![CDATA[String parameter tests. + + +For more information, visit http://docs.are/unavailable.html]]> + diff --git a/tests/test_galaxy_cli.py b/tests/test_galaxy_cli.py new file mode 100644 index 00000000..51de457a --- /dev/null +++ b/tests/test_galaxy_cli.py @@ -0,0 +1,64 @@ +import unittest +import os +import subprocess +import tempfile + +def to_test_data(*args): + return os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), "test-data", *args)) + +def file2list(pth): + with open(pth) as f: + lines = f.readlines() + return lines + +class GalaxyCliTestCase(unittest.TestCase): + + def _compare_cli_output(self, fileprefix): + in_pth = to_test_data('{}.ctd'.format(fileprefix)) + macro_pth = to_test_data('macros.xml') + tmp = tempfile.mkdtemp() + + out_file = os.path.join(tmp, '{}.xml'.format(fileprefix)) + #out_file = to_test_data('{}.xml'.format(fileprefix)) + + cmd = ['CTDConverter', 'galaxy', '-i', in_pth, '-o', out_file, '-m', macro_pth, '-b', 'version'] + print(cmd) + + popen = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) + output, err = popen.communicate() + print(output) + print(err) + + old_file_pth = to_test_data('{}.xml'.format(fileprefix)) + + print(out_file) + print(old_file_pth) + + new_l = file2list(out_file) + old_l = file2list(old_file_pth) + + for i in range(0, len(new_l)): + self.assertEqual(new_l[i].rstrip(), old_l[i].rstrip()) + + def test_galaxy_cli_full_file_ctd(self): + self._compare_cli_output('AccurateMassSearch') + + def test_galaxy_cli_empty_ctd(self): + self._compare_cli_output('empty') + + def test_galaxy_cli_float_ctd(self): + self._compare_cli_output('float') + + def test_galaxy_cli_integer_ctd(self): + self._compare_cli_output('integer') + + def test_galaxy_cli_select_ctd(self): + self._compare_cli_output('select') + + def test_galaxy_cli_string_ctd(self): + self._compare_cli_output('string') + + + +if __name__ == '__main__': + unittest.main() From 572de0c21a561f0e5f61614d1492c05715483b0f Mon Sep 17 00:00:00 2001 From: M Bernt Date: Mon, 15 Jul 2019 14:14:16 +0200 Subject: [PATCH 03/11] switch CTDopts branch --- .travis.yml | 3 +- test-data/empty.ctd | 12 ---- test-data/empty.xml | 25 ------- test-data/float.ctd | 47 ------------- test-data/float.xml | 158 ------------------------------------------ test-data/integer.ctd | 47 ------------- test-data/integer.xml | 158 ------------------------------------------ test-data/macros.xml | 31 --------- test-data/select.ctd | 20 ------ test-data/select.xml | 134 ----------------------------------- test-data/string.ctd | 20 ------ test-data/string.xml | 118 ------------------------------- 12 files changed, 2 insertions(+), 771 deletions(-) delete mode 100644 test-data/empty.ctd delete mode 100644 test-data/empty.xml delete mode 100644 test-data/float.ctd delete mode 100644 test-data/float.xml delete mode 100644 test-data/integer.ctd delete mode 100644 test-data/integer.xml delete mode 100644 test-data/macros.xml delete mode 100644 test-data/select.ctd delete mode 100644 test-data/select.xml delete mode 100644 test-data/string.ctd delete mode 100644 test-data/string.xml diff --git a/.travis.yml b/.travis.yml index 340840cf..ef5aea5c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -23,7 +23,8 @@ install: - conda config --add channels anaconda - conda config --add channels workflowconversion - - git clone https://github.com/WorkflowConversion/CTDopts $HOME/CTDopts +# - git clone https://github.com/WorkflowConversion/CTDopts $HOME/CTDopts + - git clone -b empty_numeric_defaults https://github.com/bernt-matthias/CTDopts $HOME/CTDopts - cd $HOME/CTDopts - python setup.py install - conda install -c conda-forge lxml diff --git a/test-data/empty.ctd b/test-data/empty.ctd deleted file mode 100644 index 316502e3..00000000 --- a/test-data/empty.ctd +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - - - - diff --git a/test-data/empty.xml b/test-data/empty.xml deleted file mode 100644 index 07e534e7..00000000 --- a/test-data/empty.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - - - String parameter tests - - echo StringTest - macros.xml - - - - - <![CDATA[echo StringTest - -> $param_stdout -]]> - - - - - <![CDATA[String parameter tests. - - -For more information, visit http://docs.are/unavailable.html]]> - diff --git a/test-data/float.ctd b/test-data/float.ctd deleted file mode 100644 index 2ab6c54d..00000000 --- a/test-data/float.ctd +++ /dev/null @@ -1,47 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/test-data/float.xml b/test-data/float.xml deleted file mode 100644 index f4fa7405..00000000 --- a/test-data/float.xml +++ /dev/null @@ -1,158 +0,0 @@ - - - - - Floateger parameter tests - - echo FloatTest - macros.xml - - - - - <![CDATA[echo FloatTest - -#if str($param_param_wodefault_mandatory_unrestricted): - -param_wodefault_mandatory_unrestricted $param_param_wodefault_mandatory_unrestricted -#end if -#if str($param_param_default_mandatory_unrestricted): - -param_default_mandatory_unrestricted $param_param_default_mandatory_unrestricted -#end if -#if str($param_param_wodefault_optional_unrestricted): - -param_wodefault_optional_unrestricted $param_param_wodefault_optional_unrestricted -#end if -#if str($param_param_default_optional_unrestricted): - -param_default_optional_unrestricted $param_param_default_optional_unrestricted -#end if -#if str($param_param_wodefault_mandatory_unrestricted_min): - -param_wodefault_mandatory_unrestricted_min $param_param_wodefault_mandatory_unrestricted_min -#end if -#if str($param_param_default_mandatory_unrestricted_min): - -param_default_mandatory_unrestricted_min $param_param_default_mandatory_unrestricted_min -#end if -#if str($param_param_wodefault_optional_unrestricted_min): - -param_wodefault_optional_unrestricted_min $param_param_wodefault_optional_unrestricted_min -#end if -#if str($param_param_default_optional_unrestricted_min): - -param_default_optional_unrestricted_min $param_param_default_optional_unrestricted_min -#end if -#if str($param_param_wodefault_mandatory_unrestricted_max): - -param_wodefault_mandatory_unrestricted_max $param_param_wodefault_mandatory_unrestricted_max -#end if -#if str($param_param_default_mandatory_unrestricted_max): - -param_default_mandatory_unrestricted_max $param_param_default_mandatory_unrestricted_max -#end if -#if str($param_param_wodefault_optional_unrestricted_max): - -param_wodefault_optional_unrestricted_max $param_param_wodefault_optional_unrestricted_max -#end if -#if str($param_param_default_optional_unrestricted_max): - -param_default_optional_unrestricted_max $param_param_default_optional_unrestricted_max -#end if -#if str($param_param_wodefault_mandatory_unrestricted_minmax): - -param_wodefault_mandatory_unrestricted_minmax $param_param_wodefault_mandatory_unrestricted_minmax -#end if -#if str($param_param_default_mandatory_unrestricted_minmax): - -param_default_mandatory_unrestricted_minmax $param_param_default_mandatory_unrestricted_minmax -#end if -#if str($param_param_wodefault_optional_unrestricted_minmax): - -param_wodefault_optional_unrestricted_minmax $param_param_wodefault_optional_unrestricted_minmax -#end if -#if str($param_param_default_optional_unrestricted_minmax): - -param_default_optional_unrestricted_minmax $param_param_default_optional_unrestricted_minmax -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv): - -param_wodefault_mandatory_unrestricted_adv $adv_opts.param_param_wodefault_mandatory_unrestricted_adv -#end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv): - -param_default_mandatory_unrestricted_adv $adv_opts.param_param_default_mandatory_unrestricted_adv -#end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv): - -param_wodefault_optional_unrestricted_adv $adv_opts.param_param_wodefault_optional_unrestricted_adv -#end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv): - -param_default_optional_unrestricted_adv $adv_opts.param_param_default_optional_unrestricted_adv -#end if - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min): - -param_wodefault_mandatory_unrestricted_adv_min $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min -#end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_min): - -param_default_mandatory_unrestricted_adv_min $adv_opts.param_param_default_mandatory_unrestricted_adv_min -#end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_min): - -param_wodefault_optional_unrestricted_adv_min $adv_opts.param_param_wodefault_optional_unrestricted_adv_min -#end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv_min): - -param_default_optional_unrestricted_adv_min $adv_opts.param_param_default_optional_unrestricted_adv_min -#end if - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max): - -param_wodefault_mandatory_unrestricted_adv_max $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max -#end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_max): - -param_default_mandatory_unrestricted_adv_max $adv_opts.param_param_default_mandatory_unrestricted_adv_max -#end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_max): - -param_wodefault_optional_unrestricted_adv_max $adv_opts.param_param_wodefault_optional_unrestricted_adv_max -#end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv_max): - -param_default_optional_unrestricted_adv_max $adv_opts.param_param_default_optional_unrestricted_adv_max -#end if - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax): - -param_wodefault_mandatory_unrestricted_adv_minmax $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax -#end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_minmax): - -param_default_mandatory_unrestricted_adv_minmax $adv_opts.param_param_default_mandatory_unrestricted_adv_minmax -#end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax): - -param_wodefault_optional_unrestricted_adv_minmax $adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax -#end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv_minmax): - -param_default_optional_unrestricted_adv_minmax $adv_opts.param_param_default_optional_unrestricted_adv_minmax -#end if -#end if -> $param_stdout -]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - <![CDATA[Floateger parameter tests. - - -For more information, visit http://docs.are/unavailable.html]]> - diff --git a/test-data/integer.ctd b/test-data/integer.ctd deleted file mode 100644 index 356b58da..00000000 --- a/test-data/integer.ctd +++ /dev/null @@ -1,47 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/test-data/integer.xml b/test-data/integer.xml deleted file mode 100644 index 4ae33636..00000000 --- a/test-data/integer.xml +++ /dev/null @@ -1,158 +0,0 @@ - - - - - Integer parameter tests - - echo IntTest - macros.xml - - - - - <![CDATA[echo IntTest - -#if str($param_param_wodefault_mandatory_unrestricted): - -param_wodefault_mandatory_unrestricted $param_param_wodefault_mandatory_unrestricted -#end if -#if str($param_param_default_mandatory_unrestricted): - -param_default_mandatory_unrestricted $param_param_default_mandatory_unrestricted -#end if -#if str($param_param_wodefault_optional_unrestricted): - -param_wodefault_optional_unrestricted $param_param_wodefault_optional_unrestricted -#end if -#if str($param_param_default_optional_unrestricted): - -param_default_optional_unrestricted $param_param_default_optional_unrestricted -#end if -#if str($param_param_wodefault_mandatory_unrestricted_min): - -param_wodefault_mandatory_unrestricted_min $param_param_wodefault_mandatory_unrestricted_min -#end if -#if str($param_param_default_mandatory_unrestricted_min): - -param_default_mandatory_unrestricted_min $param_param_default_mandatory_unrestricted_min -#end if -#if str($param_param_wodefault_optional_unrestricted_min): - -param_wodefault_optional_unrestricted_min $param_param_wodefault_optional_unrestricted_min -#end if -#if str($param_param_default_optional_unrestricted_min): - -param_default_optional_unrestricted_min $param_param_default_optional_unrestricted_min -#end if -#if str($param_param_wodefault_mandatory_unrestricted_max): - -param_wodefault_mandatory_unrestricted_max $param_param_wodefault_mandatory_unrestricted_max -#end if -#if str($param_param_default_mandatory_unrestricted_max): - -param_default_mandatory_unrestricted_max $param_param_default_mandatory_unrestricted_max -#end if -#if str($param_param_wodefault_optional_unrestricted_max): - -param_wodefault_optional_unrestricted_max $param_param_wodefault_optional_unrestricted_max -#end if -#if str($param_param_default_optional_unrestricted_max): - -param_default_optional_unrestricted_max $param_param_default_optional_unrestricted_max -#end if -#if str($param_param_wodefault_mandatory_unrestricted_minmax): - -param_wodefault_mandatory_unrestricted_minmax $param_param_wodefault_mandatory_unrestricted_minmax -#end if -#if str($param_param_default_mandatory_unrestricted_minmax): - -param_default_mandatory_unrestricted_minmax $param_param_default_mandatory_unrestricted_minmax -#end if -#if str($param_param_wodefault_optional_unrestricted_minmax): - -param_wodefault_optional_unrestricted_minmax $param_param_wodefault_optional_unrestricted_minmax -#end if -#if str($param_param_default_optional_unrestricted_minmax): - -param_default_optional_unrestricted_minmax $param_param_default_optional_unrestricted_minmax -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv): - -param_wodefault_mandatory_unrestricted_adv $adv_opts.param_param_wodefault_mandatory_unrestricted_adv -#end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv): - -param_default_mandatory_unrestricted_adv $adv_opts.param_param_default_mandatory_unrestricted_adv -#end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv): - -param_wodefault_optional_unrestricted_adv $adv_opts.param_param_wodefault_optional_unrestricted_adv -#end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv): - -param_default_optional_unrestricted_adv $adv_opts.param_param_default_optional_unrestricted_adv -#end if - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min): - -param_wodefault_mandatory_unrestricted_adv_min $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min -#end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_min): - -param_default_mandatory_unrestricted_adv_min $adv_opts.param_param_default_mandatory_unrestricted_adv_min -#end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_min): - -param_wodefault_optional_unrestricted_adv_min $adv_opts.param_param_wodefault_optional_unrestricted_adv_min -#end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv_min): - -param_default_optional_unrestricted_adv_min $adv_opts.param_param_default_optional_unrestricted_adv_min -#end if - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max): - -param_wodefault_mandatory_unrestricted_adv_max $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max -#end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_max): - -param_default_mandatory_unrestricted_adv_max $adv_opts.param_param_default_mandatory_unrestricted_adv_max -#end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_max): - -param_wodefault_optional_unrestricted_adv_max $adv_opts.param_param_wodefault_optional_unrestricted_adv_max -#end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv_max): - -param_default_optional_unrestricted_adv_max $adv_opts.param_param_default_optional_unrestricted_adv_max -#end if - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax): - -param_wodefault_mandatory_unrestricted_adv_minmax $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax -#end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_minmax): - -param_default_mandatory_unrestricted_adv_minmax $adv_opts.param_param_default_mandatory_unrestricted_adv_minmax -#end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax): - -param_wodefault_optional_unrestricted_adv_minmax $adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax -#end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv_minmax): - -param_default_optional_unrestricted_adv_minmax $adv_opts.param_param_default_optional_unrestricted_adv_minmax -#end if -#end if -> $param_stdout -]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - <![CDATA[Integer parameter tests. - - -For more information, visit http://docs.are/unavailable.html]]> - diff --git a/test-data/macros.xml b/test-data/macros.xml deleted file mode 100644 index 82907e42..00000000 --- a/test-data/macros.xml +++ /dev/null @@ -1,31 +0,0 @@ - - - - - requirement - - - - - - - - - - - doi:10.1186/1471-2105-9-163 - - - - - - - - - - - - - - - diff --git a/test-data/select.ctd b/test-data/select.ctd deleted file mode 100644 index f141dd12..00000000 --- a/test-data/select.ctd +++ /dev/null @@ -1,20 +0,0 @@ - - - - - - - - - - - - - - - - - - - - diff --git a/test-data/select.xml b/test-data/select.xml deleted file mode 100644 index d79bf0f2..00000000 --- a/test-data/select.xml +++ /dev/null @@ -1,134 +0,0 @@ - - - - - String parameter tests - - echo SelectTest - macros.xml - - - - - <![CDATA[echo SelectTest - -#if $param_param_wodefault_mandatory_restricted: - -param_wodefault_mandatory_restricted - #if " " in str($param_param_wodefault_mandatory_restricted): - "$param_param_wodefault_mandatory_restricted" - #else - $param_param_wodefault_mandatory_restricted - #end if -#end if -#if $param_param_default_mandatory_restricted: - -param_default_mandatory_restricted - #if " " in str($param_param_default_mandatory_restricted): - "$param_param_default_mandatory_restricted" - #else - $param_param_default_mandatory_restricted - #end if -#end if -#if $param_param_wodefault_optional_restricted: - -param_wodefault_optional_restricted - #if " " in str($param_param_wodefault_optional_restricted): - "$param_param_wodefault_optional_restricted" - #else - $param_param_wodefault_optional_restricted - #end if -#end if -#if $param_param_default_optional_restricted: - -param_default_optional_restricted - #if " " in str($param_param_default_optional_restricted): - "$param_param_default_optional_restricted" - #else - $param_param_default_optional_restricted - #end if -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_param_wodefault_mandatory_restricted_adv: - -param_wodefault_mandatory_restricted_adv - #if " " in str($adv_opts.param_param_wodefault_mandatory_restricted_adv): - "$adv_opts.param_param_wodefault_mandatory_restricted_adv" - #else - $adv_opts.param_param_wodefault_mandatory_restricted_adv - #end if -#end if - #if $adv_opts.param_param_default_mandatory_restricted_adv: - -param_default_mandatory_restricted_adv - #if " " in str($adv_opts.param_param_default_mandatory_restricted_adv): - "$adv_opts.param_param_default_mandatory_restricted_adv" - #else - $adv_opts.param_param_default_mandatory_restricted_adv - #end if -#end if - #if $adv_opts.param_param_wodefault_optional_restricted_adv: - -param_wodefault_optional_restricted_adv - #if " " in str($adv_opts.param_param_wodefault_optional_restricted_adv): - "$adv_opts.param_param_wodefault_optional_restricted_adv" - #else - $adv_opts.param_param_wodefault_optional_restricted_adv - #end if -#end if - #if $adv_opts.param_param_default_optional_restricted_adv: - -param_default_optional_restricted_adv - #if " " in str($adv_opts.param_param_default_optional_restricted_adv): - "$adv_opts.param_param_default_optional_restricted_adv" - #else - $adv_opts.param_param_default_optional_restricted_adv - #end if -#end if -#end if -> $param_stdout -]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - <![CDATA[String parameter tests. - - -For more information, visit http://docs.are/unavailable.html]]> - diff --git a/test-data/string.ctd b/test-data/string.ctd deleted file mode 100644 index 11517f36..00000000 --- a/test-data/string.ctd +++ /dev/null @@ -1,20 +0,0 @@ - - - - - - - - - - - - - - - - - - - - diff --git a/test-data/string.xml b/test-data/string.xml deleted file mode 100644 index 67109ad6..00000000 --- a/test-data/string.xml +++ /dev/null @@ -1,118 +0,0 @@ - - - - - String parameter tests - - echo StringTest - macros.xml - - - - - <![CDATA[echo StringTest - -#if str($param_param_wodefault_mandatory_unrestricted): - -param_wodefault_mandatory_unrestricted "$param_param_wodefault_mandatory_unrestricted" -#end if -#if str($param_param_default_mandatory_unrestricted): - -param_default_mandatory_unrestricted "$param_param_default_mandatory_unrestricted" -#end if -#if str($param_param_wodefault_optional_unrestricted): - -param_wodefault_optional_unrestricted "$param_param_wodefault_optional_unrestricted" -#end if -#if str($param_param_default_optional_unrestricted): - -param_default_optional_unrestricted "$param_param_default_optional_unrestricted" -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv): - -param_wodefault_mandatory_unrestricted_adv "$adv_opts.param_param_wodefault_mandatory_unrestricted_adv" -#end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv): - -param_default_mandatory_unrestricted_adv "$adv_opts.param_param_default_mandatory_unrestricted_adv" -#end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv): - -param_wodefault_optional_unrestricted_adv "$adv_opts.param_param_wodefault_optional_unrestricted_adv" -#end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv): - -param_default_optional_unrestricted_adv "$adv_opts.param_param_default_optional_unrestricted_adv" -#end if -#end if -> $param_stdout -]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - <![CDATA[String parameter tests. - - -For more information, visit http://docs.are/unavailable.html]]> - From c0089059576c8c928d387d56bd0083b7f9acbaba Mon Sep 17 00:00:00 2001 From: M Bernt Date: Mon, 15 Jul 2019 14:17:51 +0200 Subject: [PATCH 04/11] fixed CTDopts branch name --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index ef5aea5c..be252d41 100644 --- a/.travis.yml +++ b/.travis.yml @@ -24,7 +24,7 @@ install: - conda config --add channels workflowconversion # - git clone https://github.com/WorkflowConversion/CTDopts $HOME/CTDopts - - git clone -b empty_numeric_defaults https://github.com/bernt-matthias/CTDopts $HOME/CTDopts + - git clone -b topic/empty_numeric_defaults https://github.com/bernt-matthias/CTDopts $HOME/CTDopts - cd $HOME/CTDopts - python setup.py install - conda install -c conda-forge lxml From ccd6f73c1bc3d53ab3bf763550af87d435c11f3f Mon Sep 17 00:00:00 2001 From: M Bernt Date: Mon, 15 Jul 2019 14:30:34 +0200 Subject: [PATCH 05/11] improved indentation of float.ctd --- tests/test-data/float.ctd | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/tests/test-data/float.ctd b/tests/test-data/float.ctd index 2ab6c54d..ac578bda 100644 --- a/tests/test-data/float.ctd +++ b/tests/test-data/float.ctd @@ -3,45 +3,45 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - + - + - + - + From 992f45071a0974ef57c496133c4d2cf4f7a8ec52 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Mon, 15 Jul 2019 15:38:15 +0200 Subject: [PATCH 06/11] update test results --- tests/test-data/empty.xml | 8 ++--- tests/test-data/float.xml | 72 ++++++++++++++++++------------------- tests/test-data/integer.xml | 72 ++++++++++++++++++------------------- tests/test-data/select.xml | 24 ++++++------- tests/test-data/string.xml | 24 ++++++------- 5 files changed, 100 insertions(+), 100 deletions(-) diff --git a/tests/test-data/empty.xml b/tests/test-data/empty.xml index 07e534e7..e7daf119 100644 --- a/tests/test-data/empty.xml +++ b/tests/test-data/empty.xml @@ -10,16 +10,16 @@ - <![CDATA[echo StringTest + echo StringTest > $param_stdout -]]> + - <![CDATA[String parameter tests. + String parameter tests. -For more information, visit http://docs.are/unavailable.html]]> +For more information, visit http://docs.are/unavailable.html diff --git a/tests/test-data/float.xml b/tests/test-data/float.xml index f4fa7405..1fe902f6 100644 --- a/tests/test-data/float.xml +++ b/tests/test-data/float.xml @@ -10,7 +10,7 @@ - <![CDATA[echo FloatTest + echo FloatTest #if str($param_param_wodefault_mandatory_unrestricted): -param_wodefault_mandatory_unrestricted $param_param_wodefault_mandatory_unrestricted @@ -111,48 +111,48 @@ #end if #end if > $param_stdout -]]> + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - <![CDATA[Floateger parameter tests. + Floateger parameter tests. -For more information, visit http://docs.are/unavailable.html]]> +For more information, visit http://docs.are/unavailable.html diff --git a/tests/test-data/integer.xml b/tests/test-data/integer.xml index 4ae33636..e423d597 100644 --- a/tests/test-data/integer.xml +++ b/tests/test-data/integer.xml @@ -10,7 +10,7 @@ - <![CDATA[echo IntTest + echo IntTest #if str($param_param_wodefault_mandatory_unrestricted): -param_wodefault_mandatory_unrestricted $param_param_wodefault_mandatory_unrestricted @@ -111,48 +111,48 @@ #end if #end if > $param_stdout -]]> + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - <![CDATA[Integer parameter tests. + Integer parameter tests. -For more information, visit http://docs.are/unavailable.html]]> +For more information, visit http://docs.are/unavailable.html diff --git a/tests/test-data/select.xml b/tests/test-data/select.xml index d79bf0f2..437c68ba 100644 --- a/tests/test-data/select.xml +++ b/tests/test-data/select.xml @@ -10,7 +10,7 @@ - <![CDATA[echo SelectTest + echo SelectTest #if $param_param_wodefault_mandatory_restricted: -param_wodefault_mandatory_restricted @@ -79,45 +79,45 @@ #end if #end if > $param_stdout -]]> + - + - + - + - + - + - + - + - + @@ -127,8 +127,8 @@ - <![CDATA[String parameter tests. + String parameter tests. -For more information, visit http://docs.are/unavailable.html]]> +For more information, visit http://docs.are/unavailable.html diff --git a/tests/test-data/string.xml b/tests/test-data/string.xml index 67109ad6..90896ddb 100644 --- a/tests/test-data/string.xml +++ b/tests/test-data/string.xml @@ -10,7 +10,7 @@ - <![CDATA[echo StringTest + echo StringTest #if str($param_param_wodefault_mandatory_unrestricted): -param_wodefault_mandatory_unrestricted "$param_param_wodefault_mandatory_unrestricted" @@ -39,9 +39,9 @@ #end if #end if > $param_stdout -]]> + - + @@ -49,7 +49,7 @@ - + @@ -57,7 +57,7 @@ - + @@ -65,7 +65,7 @@ - + @@ -74,7 +74,7 @@ - + @@ -82,7 +82,7 @@ - + @@ -90,7 +90,7 @@ - + @@ -98,7 +98,7 @@ - + @@ -111,8 +111,8 @@ - <![CDATA[String parameter tests. + String parameter tests. -For more information, visit http://docs.are/unavailable.html]]> +For more information, visit http://docs.are/unavailable.html From fb0398ff320f1b605f34c78f5cbba42097cc805a Mon Sep 17 00:00:00 2001 From: M Bernt Date: Mon, 15 Jul 2019 16:39:25 +0200 Subject: [PATCH 07/11] added test files for bool, in/out files --- tests/test-data/bool.ctd | 17 +++++++ tests/test-data/bool.xml | 62 ++++++++++++++++++++++++++ tests/test-data/ifile.ctd | 28 ++++++++++++ tests/test-data/ifile.xml | 94 +++++++++++++++++++++++++++++++++++++++ tests/test-data/ofile.ctd | 28 ++++++++++++ tests/test-data/ofile.xml | 87 ++++++++++++++++++++++++++++++++++++ 6 files changed, 316 insertions(+) create mode 100644 tests/test-data/bool.ctd create mode 100644 tests/test-data/bool.xml create mode 100644 tests/test-data/ifile.ctd create mode 100644 tests/test-data/ifile.xml create mode 100644 tests/test-data/ofile.ctd create mode 100644 tests/test-data/ofile.xml diff --git a/tests/test-data/bool.ctd b/tests/test-data/bool.ctd new file mode 100644 index 00000000..a9f46f32 --- /dev/null +++ b/tests/test-data/bool.ctd @@ -0,0 +1,17 @@ + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/bool.xml b/tests/test-data/bool.xml new file mode 100644 index 00000000..4139fbcc --- /dev/null +++ b/tests/test-data/bool.xml @@ -0,0 +1,62 @@ + + + + + String parameter tests + + echo StringTest + macros.xml + + + + + echo StringTest + +#if $param_param_true_optional_unrestricted: + -param_true_optional_unrestricted + #if " " in str($param_param_true_optional_unrestricted): + "$param_param_true_optional_unrestricted" + #else + $param_param_true_optional_unrestricted + #end if +#end if +#if $param_param_false_optional_unrestricted: + -param_false_optional_unrestricted +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_param_true_optional_unrestricted_adv: + -param_true_optional_unrestricted_adv + #if " " in str($adv_opts.param_param_true_optional_unrestricted_adv): + "$adv_opts.param_param_true_optional_unrestricted_adv" + #else + $adv_opts.param_param_true_optional_unrestricted_adv + #end if +#end if + #if $adv_opts.param_param_false_optional_unrestricted_adv: + -param_false_optional_unrestricted_adv +#end if +#end if +> $param_stdout + + + + + + + + + + + + + + + + + + + String parameter tests. + + +For more information, visit http://docs.are/unavailable.html + diff --git a/tests/test-data/ifile.ctd b/tests/test-data/ifile.ctd new file mode 100644 index 00000000..3ff8d7d6 --- /dev/null +++ b/tests/test-data/ifile.ctd @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/ifile.xml b/tests/test-data/ifile.xml new file mode 100644 index 00000000..f1b379dc --- /dev/null +++ b/tests/test-data/ifile.xml @@ -0,0 +1,94 @@ + + + + + Input File parameter tests + + echo inFileTest + macros.xml + + + + + echo inFileTest + +#if str($param_param_wodefault_mandatory_unrestricted_noformat): + -param_wodefault_mandatory_unrestricted_noformat $param_param_wodefault_mandatory_unrestricted_noformat +#end if +#if str($param_param_default_mandatory_unrestricted_noformat): + -param_default_mandatory_unrestricted_noformat $param_param_default_mandatory_unrestricted_noformat +#end if +#if str($param_param_wodefault_optional_unrestricted_noformat): + -param_wodefault_optional_unrestricted_noformat $param_param_wodefault_optional_unrestricted_noformat +#end if +#if str($param_param_default_optional_unrestricted_noformat): + -param_default_optional_unrestricted_noformat $param_param_default_optional_unrestricted_noformat +#end if +#if str($param_param_wodefault_mandatory_unrestricted_multformat): + -param_wodefault_mandatory_unrestricted_multformat $param_param_wodefault_mandatory_unrestricted_multformat +#end if +#if str($param_param_default_mandatory_unrestricted_multformat): + -param_default_mandatory_unrestricted_multformat $param_param_default_mandatory_unrestricted_multformat +#end if +#if str($param_param_wodefault_optional_unrestricted_multformat): + -param_wodefault_optional_unrestricted_multformat $param_param_wodefault_optional_unrestricted_multformat +#end if +#if str($param_param_default_optional_unrestricted_multformat): + -param_default_optional_unrestricted_multformat $param_param_default_optional_unrestricted_multformat +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_noformat): + -param_wodefault_mandatory_unrestricted_adv_noformat $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_noformat +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_noformat): + -param_default_mandatory_unrestricted_adv_noformat $adv_opts.param_param_default_mandatory_unrestricted_adv_noformat +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_noformat): + -param_wodefault_optional_unrestricted_adv_noformat $adv_opts.param_param_wodefault_optional_unrestricted_adv_noformat +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_noformat): + -param_default_optional_unrestricted_adv_noformat $adv_opts.param_param_default_optional_unrestricted_adv_noformat +#end if + #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_multformat): + -param_wodefault_mandatory_unrestricted_adv_multformat $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_multformat +#end if + #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_multformat): + -param_default_mandatory_unrestricted_adv_multformat $adv_opts.param_param_default_mandatory_unrestricted_adv_multformat +#end if + #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_multformat): + -param_wodefault_optional_unrestricted_adv_multformat $adv_opts.param_param_wodefault_optional_unrestricted_adv_multformat +#end if + #if str($adv_opts.param_param_default_optional_unrestricted_adv_multformat): + -param_default_optional_unrestricted_adv_multformat $adv_opts.param_param_default_optional_unrestricted_adv_multformat +#end if +#end if +> $param_stdout + + + + + + + + + + + + + + + + + + + + + + + + + Input File parameter tests. + + +For more information, visit http://docs.are/unavailable.html + diff --git a/tests/test-data/ofile.ctd b/tests/test-data/ofile.ctd new file mode 100644 index 00000000..f7fff8fa --- /dev/null +++ b/tests/test-data/ofile.ctd @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/ofile.xml b/tests/test-data/ofile.xml new file mode 100644 index 00000000..f2ec74e7 --- /dev/null +++ b/tests/test-data/ofile.xml @@ -0,0 +1,87 @@ + + + + + Input File parameter tests + + echo outFileTest + macros.xml + + + + + echo outFileTest + +#if str($param_param_wodefault_mandatory_unrestricted_snglformat): + -param_wodefault_mandatory_unrestricted_snglformat $param_param_wodefault_mandatory_unrestricted_snglformat +#end if +#if str($param_param_default_mandatory_unrestricted_snglformat): + -param_default_mandatory_unrestricted_snglformat $param_param_default_mandatory_unrestricted_snglformat +#end if +#if str($param_param_wodefault_optional_unrestricted_snglformat): + -param_wodefault_optional_unrestricted_snglformat $param_param_wodefault_optional_unrestricted_snglformat +#end if +#if str($param_param_default_optional_unrestricted_snglformat): + -param_default_optional_unrestricted_snglformat $param_param_default_optional_unrestricted_snglformat +#end if +#if str($param_param_wodefault_mandatory_unrestricted_adv_snglformat): + -param_wodefault_mandatory_unrestricted_adv_snglformat $param_param_wodefault_mandatory_unrestricted_adv_snglformat +#end if +#if str($param_param_default_mandatory_unrestricted_adv_snglformat): + -param_default_mandatory_unrestricted_adv_snglformat $param_param_default_mandatory_unrestricted_adv_snglformat +#end if +#if str($param_param_wodefault_optional_unrestricted_adv_snglformat): + -param_wodefault_optional_unrestricted_adv_snglformat $param_param_wodefault_optional_unrestricted_adv_snglformat +#end if +#if str($param_param_default_optional_unrestricted_adv_snglformat): + -param_default_optional_unrestricted_adv_snglformat $param_param_default_optional_unrestricted_adv_snglformat +#end if +#if str($param_param_wodefault_mandatory_unrestricted_multformat): + -param_wodefault_mandatory_unrestricted_multformat $param_param_wodefault_mandatory_unrestricted_multformat +#end if +#if str($param_param_default_mandatory_unrestricted_multformat): + -param_default_mandatory_unrestricted_multformat $param_param_default_mandatory_unrestricted_multformat +#end if +#if str($param_param_wodefault_optional_unrestricted_multformat): + -param_wodefault_optional_unrestricted_multformat $param_param_wodefault_optional_unrestricted_multformat +#end if +#if str($param_param_default_optional_unrestricted_multformat): + -param_default_optional_unrestricted_multformat $param_param_default_optional_unrestricted_multformat +#end if +#if str($param_param_wodefault_mandatory_unrestricted_adv_multformat): + -param_wodefault_mandatory_unrestricted_adv_multformat $param_param_wodefault_mandatory_unrestricted_adv_multformat +#end if +#if str($param_param_default_mandatory_unrestricted_adv_multformat): + -param_default_mandatory_unrestricted_adv_multformat $param_param_default_mandatory_unrestricted_adv_multformat +#end if +#if str($param_param_wodefault_optional_unrestricted_adv_multformat): + -param_wodefault_optional_unrestricted_adv_multformat $param_param_wodefault_optional_unrestricted_adv_multformat +#end if +#if str($param_param_default_optional_unrestricted_adv_multformat): + -param_default_optional_unrestricted_adv_multformat $param_param_default_optional_unrestricted_adv_multformat +#end if + + + + + + + + + + + + + + + + + + + + + Input File parameter tests. + + +For more information, visit http://docs.are/unavailable.html + From 38a77676de4495539f25e56f238c23f52fdc37c9 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 16 Jul 2019 15:21:52 +0200 Subject: [PATCH 08/11] - added filetypes to test call - removed test file from OpenMS - fixed xsd link - extended select, i/o file test data --- tests/test-data/AccurateMassSearch.ctd | 44 -- tests/test-data/AccurateMassSearch.xml | 144 ---- tests/test-data/bool.ctd | 20 +- tests/test-data/bool.xml | 48 +- tests/test-data/empty.ctd | 2 +- tests/test-data/float.ctd | 2 +- tests/test-data/ifile.ctd | 62 +- tests/test-data/ifile.xml | 272 ++++++-- tests/test-data/integer.ctd | 66 +- tests/test-data/integer.xml | 192 +++--- tests/test-data/ofile.ctd | 50 +- tests/test-data/ofile.xml | 178 +++-- tests/test-data/repeat.ctd | 125 ++++ tests/test-data/repeat.xml | 866 +++++++++++++++++++++++++ tests/test-data/select.ctd | 51 +- tests/test-data/select.xml | 244 +++++-- tests/test-data/string.ctd | 2 +- tests/test_galaxy_cli.py | 3 +- 18 files changed, 1820 insertions(+), 551 deletions(-) delete mode 100644 tests/test-data/AccurateMassSearch.ctd delete mode 100644 tests/test-data/AccurateMassSearch.xml create mode 100644 tests/test-data/repeat.ctd create mode 100644 tests/test-data/repeat.xml diff --git a/tests/test-data/AccurateMassSearch.ctd b/tests/test-data/AccurateMassSearch.ctd deleted file mode 100644 index 6092d44e..00000000 --- a/tests/test-data/AccurateMassSearch.ctd +++ /dev/null @@ -1,44 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/test-data/AccurateMassSearch.xml b/tests/test-data/AccurateMassSearch.xml deleted file mode 100644 index 14bff665..00000000 --- a/tests/test-data/AccurateMassSearch.xml +++ /dev/null @@ -1,144 +0,0 @@ - - - - - Match MS signals to molecules from a database by mass. - - AccurateMassSearch - macros.xml - - - - - AccurateMassSearch - -#if str($param_in): - -in $param_in -#end if -#if str($param_out): - -out $param_out -#end if -#if str($param_out_annotation): - -out_annotation $param_out_annotation -#end if -#if str($param_positive_adducts): - -positive_adducts $param_positive_adducts -#end if -#if str($param_negative_adducts): - -negative_adducts $param_negative_adducts -#end if -#if str($param_threads): - -threads $param_threads -#end if --db:mapping - #for token in $param_db_mapping: - $token - #end for --db:struct - #for token in $param_db_struct: - $token - #end for -#if str($param_algorithm_mass_error_value): - -algorithm:mass_error_value $param_algorithm_mass_error_value -#end if -#if $param_algorithm_mass_error_unit: - -algorithm:mass_error_unit - #if " " in str($param_algorithm_mass_error_unit): - "$param_algorithm_mass_error_unit" - #else - $param_algorithm_mass_error_unit - #end if -#end if -#if $param_algorithm_ionization_mode: - -algorithm:ionization_mode - #if " " in str($param_algorithm_ionization_mode): - "$param_algorithm_ionization_mode" - #else - $param_algorithm_ionization_mode - #end if -#end if -#if $param_algorithm_isotopic_similarity: - -algorithm:isotopic_similarity -#end if -#if $param_algorithm_keep_unidentified_masses: - -algorithm:keep_unidentified_masses -#end if -#if str($param_algorithm_mzTab_exportIsotopeIntensities): - -algorithm:mzTab:exportIsotopeIntensities $param_algorithm_mzTab_exportIsotopeIntensities -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if str($adv_opts.param_log): - -log "$adv_opts.param_log" -#end if - #if str($adv_opts.param_debug): - -debug $adv_opts.param_debug -#end if - #if $adv_opts.param_no_progress: - -no_progress -#end if - #if $adv_opts.param_force: - -force -#end if - #if $adv_opts.param_test: - -test -#end if -#end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Match MS signals to molecules from a database by mass. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html - diff --git a/tests/test-data/bool.ctd b/tests/test-data/bool.ctd index a9f46f32..d59641e2 100644 --- a/tests/test-data/bool.ctd +++ b/tests/test-data/bool.ctd @@ -1,16 +1,16 @@ - - - - - + + + + + - + - - - - + + + + diff --git a/tests/test-data/bool.xml b/tests/test-data/bool.xml index 4139fbcc..30674b85 100644 --- a/tests/test-data/bool.xml +++ b/tests/test-data/bool.xml @@ -1,61 +1,61 @@ - - - String parameter tests + + + Bool parameter tests - echo StringTest + echo BoolTest macros.xml - echo StringTest + echo BoolTest -#if $param_param_true_optional_unrestricted: - -param_true_optional_unrestricted - #if " " in str($param_param_true_optional_unrestricted): - "$param_param_true_optional_unrestricted" +#if $param_true_optional_unrestricted: + -true_optional_unrestricted + #if " " in str($param_true_optional_unrestricted): + "$param_true_optional_unrestricted" #else - $param_param_true_optional_unrestricted + $param_true_optional_unrestricted #end if #end if -#if $param_param_false_optional_unrestricted: - -param_false_optional_unrestricted +#if $param_false_optional_unrestricted: + -false_optional_unrestricted #end if #if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_param_true_optional_unrestricted_adv: - -param_true_optional_unrestricted_adv - #if " " in str($adv_opts.param_param_true_optional_unrestricted_adv): - "$adv_opts.param_param_true_optional_unrestricted_adv" + #if $adv_opts.param_true_optional_unrestricted_adv: + -true_optional_unrestricted_adv + #if " " in str($adv_opts.param_true_optional_unrestricted_adv): + "$adv_opts.param_true_optional_unrestricted_adv" #else - $adv_opts.param_param_true_optional_unrestricted_adv + $adv_opts.param_true_optional_unrestricted_adv #end if #end if - #if $adv_opts.param_param_false_optional_unrestricted_adv: - -param_false_optional_unrestricted_adv + #if $adv_opts.param_false_optional_unrestricted_adv: + -false_optional_unrestricted_adv #end if #end if > $param_stdout - + - + - + - + - String parameter tests. + Bool parameter tests. For more information, visit http://docs.are/unavailable.html diff --git a/tests/test-data/empty.ctd b/tests/test-data/empty.ctd index 316502e3..1ffc19de 100644 --- a/tests/test-data/empty.ctd +++ b/tests/test-data/empty.ctd @@ -2,7 +2,7 @@ - + diff --git a/tests/test-data/float.ctd b/tests/test-data/float.ctd index ac578bda..af537d83 100644 --- a/tests/test-data/float.ctd +++ b/tests/test-data/float.ctd @@ -2,7 +2,7 @@ - + diff --git a/tests/test-data/ifile.ctd b/tests/test-data/ifile.ctd index 3ff8d7d6..be957cb9 100644 --- a/tests/test-data/ifile.ctd +++ b/tests/test-data/ifile.ctd @@ -2,26 +2,54 @@ - + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/ifile.xml b/tests/test-data/ifile.xml index f1b379dc..232b9fa0 100644 --- a/tests/test-data/ifile.xml +++ b/tests/test-data/ifile.xml @@ -12,76 +12,252 @@ echo inFileTest -#if str($param_param_wodefault_mandatory_unrestricted_noformat): - -param_wodefault_mandatory_unrestricted_noformat $param_param_wodefault_mandatory_unrestricted_noformat +#if str($param_mandatory_noformat): + -mandatory_noformat $param_mandatory_noformat #end if -#if str($param_param_default_mandatory_unrestricted_noformat): - -param_default_mandatory_unrestricted_noformat $param_param_default_mandatory_unrestricted_noformat +#if str($param_optional_noformat): + -optional_noformat $param_optional_noformat #end if -#if str($param_param_wodefault_optional_unrestricted_noformat): - -param_wodefault_optional_unrestricted_noformat $param_param_wodefault_optional_unrestricted_noformat +#if str($param_mandatory_oneformat): + -mandatory_oneformat $param_mandatory_oneformat #end if -#if str($param_param_default_optional_unrestricted_noformat): - -param_default_optional_unrestricted_noformat $param_param_default_optional_unrestricted_noformat +#if str($param_optional_oneformat): + -optional_oneformat $param_optional_oneformat #end if -#if str($param_param_wodefault_mandatory_unrestricted_multformat): - -param_wodefault_mandatory_unrestricted_multformat $param_param_wodefault_mandatory_unrestricted_multformat +#if str($param_mandatory_multformat): + -mandatory_multformat $param_mandatory_multformat #end if -#if str($param_param_default_mandatory_unrestricted_multformat): - -param_default_mandatory_unrestricted_multformat $param_param_default_mandatory_unrestricted_multformat +#if str($param_optional_multformat): + -optional_multformat $param_optional_multformat #end if -#if str($param_param_wodefault_optional_unrestricted_multformat): - -param_wodefault_optional_unrestricted_multformat $param_param_wodefault_optional_unrestricted_multformat +#if str($param_default_mandatory_noformat): + -default_mandatory_noformat $param_default_mandatory_noformat #end if -#if str($param_param_default_optional_unrestricted_multformat): - -param_default_optional_unrestricted_multformat $param_param_default_optional_unrestricted_multformat +#if str($param_default_optional_noformat): + -default_optional_noformat $param_default_optional_noformat #end if +#if str($param_default_mandatory_oneformat): + -default_mandatory_oneformat $param_default_mandatory_oneformat +#end if +#if str($param_default_optional_oneformat): + -default_optional_oneformat $param_default_optional_oneformat +#end if +#if str($param_default_mandatory_multformat): + -default_mandatory_multformat $param_default_mandatory_multformat +#end if +#if str($param_default_optional_multformat): + -default_optional_multformat $param_default_optional_multformat +#end if +-list_mandatory_noformat + #for token in $param_list_mandatory_noformat: + $token + #end for +-list_optional_noformat + #for token in $param_list_optional_noformat: + $token + #end for +-list_mandatory_oneformat + #for token in $param_list_mandatory_oneformat: + $token + #end for +-list_optional_oneformat + #for token in $param_list_optional_oneformat: + $token + #end for +-list_mandatory_multformat + #for token in $param_list_mandatory_multformat: + $token + #end for +-list_optional_multformat + #for token in $param_list_optional_multformat: + $token + #end for #if $adv_opts.adv_opts_selector=='advanced': - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_noformat): - -param_wodefault_mandatory_unrestricted_adv_noformat $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_noformat + #if str($adv_opts.param_mandatory_noformat_adv): + -mandatory_noformat_adv $adv_opts.param_mandatory_noformat_adv +#end if + #if str($adv_opts.param_optional_noformat_adv): + -optional_noformat_adv $adv_opts.param_optional_noformat_adv +#end if + #if str($adv_opts.param_mandatory_oneformat_adv): + -mandatory_oneformat_adv $adv_opts.param_mandatory_oneformat_adv +#end if + #if str($adv_opts.param_optional_oneformat_adv): + -optional_oneformat_adv $adv_opts.param_optional_oneformat_adv +#end if + #if str($adv_opts.param_mandatory_multformat_adv): + -mandatory_multformat_adv $adv_opts.param_mandatory_multformat_adv #end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_noformat): - -param_default_mandatory_unrestricted_adv_noformat $adv_opts.param_param_default_mandatory_unrestricted_adv_noformat + #if str($adv_opts.param_optional_multformat_adv): + -optional_multformat_adv $adv_opts.param_optional_multformat_adv #end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_noformat): - -param_wodefault_optional_unrestricted_adv_noformat $adv_opts.param_param_wodefault_optional_unrestricted_adv_noformat + #if str($adv_opts.param_default_mandatory_noformat_adv): + -default_mandatory_noformat_adv $adv_opts.param_default_mandatory_noformat_adv #end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv_noformat): - -param_default_optional_unrestricted_adv_noformat $adv_opts.param_param_default_optional_unrestricted_adv_noformat + #if str($adv_opts.param_default_optional_noformat_adv): + -default_optional_noformat_adv $adv_opts.param_default_optional_noformat_adv #end if - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_multformat): - -param_wodefault_mandatory_unrestricted_adv_multformat $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_multformat + #if str($adv_opts.param_default_mandatory_oneformat_adv): + -default_mandatory_oneformat_adv $adv_opts.param_default_mandatory_oneformat_adv #end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_multformat): - -param_default_mandatory_unrestricted_adv_multformat $adv_opts.param_param_default_mandatory_unrestricted_adv_multformat + #if str($adv_opts.param_default_optional_oneformat_adv): + -default_optional_oneformat_adv $adv_opts.param_default_optional_oneformat_adv #end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_multformat): - -param_wodefault_optional_unrestricted_adv_multformat $adv_opts.param_param_wodefault_optional_unrestricted_adv_multformat + #if str($adv_opts.param_default_mandatory_multformat_adv): + -default_mandatory_multformat_adv $adv_opts.param_default_mandatory_multformat_adv #end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv_multformat): - -param_default_optional_unrestricted_adv_multformat $adv_opts.param_param_default_optional_unrestricted_adv_multformat + #if str($adv_opts.param_default_optional_multformat_adv): + -default_optional_multformat_adv $adv_opts.param_default_optional_multformat_adv #end if + -list_mandatory_noformat_adv + #for token in $param_list_mandatory_noformat_adv: + $token + #end for + -list_optional_noformat_adv + #for token in $param_list_optional_noformat_adv: + $token + #end for + -list_mandatory_oneformat_adv + #for token in $param_list_mandatory_oneformat_adv: + $token + #end for + -list_optional_oneformat_adv + #for token in $param_list_optional_oneformat_adv: + $token + #end for + -list_mandatory_multformat_adv + #for token in $param_list_mandatory_multformat_adv: + $token + #end for + -list_optional_multformat_adv + #for token in $param_list_optional_multformat_adv: + $token + #end for #end if > $param_stdout - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/integer.ctd b/tests/test-data/integer.ctd index 356b58da..a358e3c6 100644 --- a/tests/test-data/integer.ctd +++ b/tests/test-data/integer.ctd @@ -2,45 +2,45 @@ - + - - - - - - - - + + + + + + + + - - - - - - - - + + + + + + + + - - - - - - - - + + + + + + + + - - - - - - - - + + + + + + + + diff --git a/tests/test-data/integer.xml b/tests/test-data/integer.xml index e423d597..bf20e9b2 100644 --- a/tests/test-data/integer.xml +++ b/tests/test-data/integer.xml @@ -12,140 +12,140 @@ echo IntTest -#if str($param_param_wodefault_mandatory_unrestricted): - -param_wodefault_mandatory_unrestricted $param_param_wodefault_mandatory_unrestricted +#if str($param_wodefault_mandatory_unrestricted): + -wodefault_mandatory_unrestricted $param_wodefault_mandatory_unrestricted #end if -#if str($param_param_default_mandatory_unrestricted): - -param_default_mandatory_unrestricted $param_param_default_mandatory_unrestricted +#if str($param_default_mandatory_unrestricted): + -default_mandatory_unrestricted $param_default_mandatory_unrestricted #end if -#if str($param_param_wodefault_optional_unrestricted): - -param_wodefault_optional_unrestricted $param_param_wodefault_optional_unrestricted +#if str($param_wodefault_optional_unrestricted): + -wodefault_optional_unrestricted $param_wodefault_optional_unrestricted #end if -#if str($param_param_default_optional_unrestricted): - -param_default_optional_unrestricted $param_param_default_optional_unrestricted +#if str($param_default_optional_unrestricted): + -default_optional_unrestricted $param_default_optional_unrestricted #end if -#if str($param_param_wodefault_mandatory_unrestricted_min): - -param_wodefault_mandatory_unrestricted_min $param_param_wodefault_mandatory_unrestricted_min +#if str($param_wodefault_mandatory_unrestricted_min): + -wodefault_mandatory_unrestricted_min $param_wodefault_mandatory_unrestricted_min #end if -#if str($param_param_default_mandatory_unrestricted_min): - -param_default_mandatory_unrestricted_min $param_param_default_mandatory_unrestricted_min +#if str($param_default_mandatory_unrestricted_min): + -default_mandatory_unrestricted_min $param_default_mandatory_unrestricted_min #end if -#if str($param_param_wodefault_optional_unrestricted_min): - -param_wodefault_optional_unrestricted_min $param_param_wodefault_optional_unrestricted_min +#if str($param_wodefault_optional_unrestricted_min): + -wodefault_optional_unrestricted_min $param_wodefault_optional_unrestricted_min #end if -#if str($param_param_default_optional_unrestricted_min): - -param_default_optional_unrestricted_min $param_param_default_optional_unrestricted_min +#if str($param_default_optional_unrestricted_min): + -default_optional_unrestricted_min $param_default_optional_unrestricted_min #end if -#if str($param_param_wodefault_mandatory_unrestricted_max): - -param_wodefault_mandatory_unrestricted_max $param_param_wodefault_mandatory_unrestricted_max +#if str($param_wodefault_mandatory_unrestricted_max): + -wodefault_mandatory_unrestricted_max $param_wodefault_mandatory_unrestricted_max #end if -#if str($param_param_default_mandatory_unrestricted_max): - -param_default_mandatory_unrestricted_max $param_param_default_mandatory_unrestricted_max +#if str($param_default_mandatory_unrestricted_max): + -default_mandatory_unrestricted_max $param_default_mandatory_unrestricted_max #end if -#if str($param_param_wodefault_optional_unrestricted_max): - -param_wodefault_optional_unrestricted_max $param_param_wodefault_optional_unrestricted_max +#if str($param_wodefault_optional_unrestricted_max): + -wodefault_optional_unrestricted_max $param_wodefault_optional_unrestricted_max #end if -#if str($param_param_default_optional_unrestricted_max): - -param_default_optional_unrestricted_max $param_param_default_optional_unrestricted_max +#if str($param_default_optional_unrestricted_max): + -default_optional_unrestricted_max $param_default_optional_unrestricted_max #end if -#if str($param_param_wodefault_mandatory_unrestricted_minmax): - -param_wodefault_mandatory_unrestricted_minmax $param_param_wodefault_mandatory_unrestricted_minmax +#if str($param_wodefault_mandatory_unrestricted_minmax): + -wodefault_mandatory_unrestricted_minmax $param_wodefault_mandatory_unrestricted_minmax #end if -#if str($param_param_default_mandatory_unrestricted_minmax): - -param_default_mandatory_unrestricted_minmax $param_param_default_mandatory_unrestricted_minmax +#if str($param_default_mandatory_unrestricted_minmax): + -default_mandatory_unrestricted_minmax $param_default_mandatory_unrestricted_minmax #end if -#if str($param_param_wodefault_optional_unrestricted_minmax): - -param_wodefault_optional_unrestricted_minmax $param_param_wodefault_optional_unrestricted_minmax +#if str($param_wodefault_optional_unrestricted_minmax): + -wodefault_optional_unrestricted_minmax $param_wodefault_optional_unrestricted_minmax #end if -#if str($param_param_default_optional_unrestricted_minmax): - -param_default_optional_unrestricted_minmax $param_param_default_optional_unrestricted_minmax +#if str($param_default_optional_unrestricted_minmax): + -default_optional_unrestricted_minmax $param_default_optional_unrestricted_minmax #end if #if $adv_opts.adv_opts_selector=='advanced': - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv): - -param_wodefault_mandatory_unrestricted_adv $adv_opts.param_param_wodefault_mandatory_unrestricted_adv + #if str($adv_opts.param_wodefault_mandatory_unrestricted_adv): + -wodefault_mandatory_unrestricted_adv $adv_opts.param_wodefault_mandatory_unrestricted_adv #end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv): - -param_default_mandatory_unrestricted_adv $adv_opts.param_param_default_mandatory_unrestricted_adv + #if str($adv_opts.param_default_mandatory_unrestricted_adv): + -default_mandatory_unrestricted_adv $adv_opts.param_default_mandatory_unrestricted_adv #end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv): - -param_wodefault_optional_unrestricted_adv $adv_opts.param_param_wodefault_optional_unrestricted_adv + #if str($adv_opts.param_wodefault_optional_unrestricted_adv): + -wodefault_optional_unrestricted_adv $adv_opts.param_wodefault_optional_unrestricted_adv #end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv): - -param_default_optional_unrestricted_adv $adv_opts.param_param_default_optional_unrestricted_adv + #if str($adv_opts.param_default_optional_unrestricted_adv): + -default_optional_unrestricted_adv $adv_opts.param_default_optional_unrestricted_adv #end if - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min): - -param_wodefault_mandatory_unrestricted_adv_min $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_min + #if str($adv_opts.param_wodefault_mandatory_unrestricted_adv_min): + -wodefault_mandatory_unrestricted_adv_min $adv_opts.param_wodefault_mandatory_unrestricted_adv_min #end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_min): - -param_default_mandatory_unrestricted_adv_min $adv_opts.param_param_default_mandatory_unrestricted_adv_min + #if str($adv_opts.param_default_mandatory_unrestricted_adv_min): + -default_mandatory_unrestricted_adv_min $adv_opts.param_default_mandatory_unrestricted_adv_min #end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_min): - -param_wodefault_optional_unrestricted_adv_min $adv_opts.param_param_wodefault_optional_unrestricted_adv_min + #if str($adv_opts.param_wodefault_optional_unrestricted_adv_min): + -wodefault_optional_unrestricted_adv_min $adv_opts.param_wodefault_optional_unrestricted_adv_min #end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv_min): - -param_default_optional_unrestricted_adv_min $adv_opts.param_param_default_optional_unrestricted_adv_min + #if str($adv_opts.param_default_optional_unrestricted_adv_min): + -default_optional_unrestricted_adv_min $adv_opts.param_default_optional_unrestricted_adv_min #end if - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max): - -param_wodefault_mandatory_unrestricted_adv_max $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_max + #if str($adv_opts.param_wodefault_mandatory_unrestricted_adv_max): + -wodefault_mandatory_unrestricted_adv_max $adv_opts.param_wodefault_mandatory_unrestricted_adv_max #end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_max): - -param_default_mandatory_unrestricted_adv_max $adv_opts.param_param_default_mandatory_unrestricted_adv_max + #if str($adv_opts.param_default_mandatory_unrestricted_adv_max): + -default_mandatory_unrestricted_adv_max $adv_opts.param_default_mandatory_unrestricted_adv_max #end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_max): - -param_wodefault_optional_unrestricted_adv_max $adv_opts.param_param_wodefault_optional_unrestricted_adv_max + #if str($adv_opts.param_wodefault_optional_unrestricted_adv_max): + -wodefault_optional_unrestricted_adv_max $adv_opts.param_wodefault_optional_unrestricted_adv_max #end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv_max): - -param_default_optional_unrestricted_adv_max $adv_opts.param_param_default_optional_unrestricted_adv_max + #if str($adv_opts.param_default_optional_unrestricted_adv_max): + -default_optional_unrestricted_adv_max $adv_opts.param_default_optional_unrestricted_adv_max #end if - #if str($adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax): - -param_wodefault_mandatory_unrestricted_adv_minmax $adv_opts.param_param_wodefault_mandatory_unrestricted_adv_minmax + #if str($adv_opts.param_wodefault_mandatory_unrestricted_adv_minmax): + -wodefault_mandatory_unrestricted_adv_minmax $adv_opts.param_wodefault_mandatory_unrestricted_adv_minmax #end if - #if str($adv_opts.param_param_default_mandatory_unrestricted_adv_minmax): - -param_default_mandatory_unrestricted_adv_minmax $adv_opts.param_param_default_mandatory_unrestricted_adv_minmax + #if str($adv_opts.param_default_mandatory_unrestricted_adv_minmax): + -default_mandatory_unrestricted_adv_minmax $adv_opts.param_default_mandatory_unrestricted_adv_minmax #end if - #if str($adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax): - -param_wodefault_optional_unrestricted_adv_minmax $adv_opts.param_param_wodefault_optional_unrestricted_adv_minmax + #if str($adv_opts.param_wodefault_optional_unrestricted_adv_minmax): + -wodefault_optional_unrestricted_adv_minmax $adv_opts.param_wodefault_optional_unrestricted_adv_minmax #end if - #if str($adv_opts.param_param_default_optional_unrestricted_adv_minmax): - -param_default_optional_unrestricted_adv_minmax $adv_opts.param_param_default_optional_unrestricted_adv_minmax + #if str($adv_opts.param_default_optional_unrestricted_adv_minmax): + -default_optional_unrestricted_adv_minmax $adv_opts.param_default_optional_unrestricted_adv_minmax #end if #end if > $param_stdout - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + diff --git a/tests/test-data/ofile.ctd b/tests/test-data/ofile.ctd index f7fff8fa..bed6a853 100644 --- a/tests/test-data/ofile.ctd +++ b/tests/test-data/ofile.ctd @@ -1,28 +1,40 @@ - + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/ofile.xml b/tests/test-data/ofile.xml index f2ec74e7..f3678f7a 100644 --- a/tests/test-data/ofile.xml +++ b/tests/test-data/ofile.xml @@ -1,6 +1,6 @@ - + Input File parameter tests @@ -12,73 +12,153 @@ echo outFileTest -#if str($param_param_wodefault_mandatory_unrestricted_snglformat): - -param_wodefault_mandatory_unrestricted_snglformat $param_param_wodefault_mandatory_unrestricted_snglformat +#if str($param_wodefault_mandatory_noformat): + -wodefault_mandatory_noformat $param_wodefault_mandatory_noformat #end if -#if str($param_param_default_mandatory_unrestricted_snglformat): - -param_default_mandatory_unrestricted_snglformat $param_param_default_mandatory_unrestricted_snglformat +#if str($param_default_mandatory_noformat): + -default_mandatory_noformat $param_default_mandatory_noformat #end if -#if str($param_param_wodefault_optional_unrestricted_snglformat): - -param_wodefault_optional_unrestricted_snglformat $param_param_wodefault_optional_unrestricted_snglformat +#if str($param_wodefault_optional_noformat): + -wodefault_optional_noformat $param_wodefault_optional_noformat #end if -#if str($param_param_default_optional_unrestricted_snglformat): - -param_default_optional_unrestricted_snglformat $param_param_default_optional_unrestricted_snglformat +#if str($param_default_optional_noformat): + -default_optional_noformat $param_default_optional_noformat #end if -#if str($param_param_wodefault_mandatory_unrestricted_adv_snglformat): - -param_wodefault_mandatory_unrestricted_adv_snglformat $param_param_wodefault_mandatory_unrestricted_adv_snglformat +#if str($param_wodefault_mandatory_oneformat): + -wodefault_mandatory_oneformat $param_wodefault_mandatory_oneformat #end if -#if str($param_param_default_mandatory_unrestricted_adv_snglformat): - -param_default_mandatory_unrestricted_adv_snglformat $param_param_default_mandatory_unrestricted_adv_snglformat +#if str($param_default_mandatory_oneformat): + -default_mandatory_oneformat $param_default_mandatory_oneformat #end if -#if str($param_param_wodefault_optional_unrestricted_adv_snglformat): - -param_wodefault_optional_unrestricted_adv_snglformat $param_param_wodefault_optional_unrestricted_adv_snglformat +#if str($param_wodefault_optional_oneformat): + -wodefault_optional_oneformat $param_wodefault_optional_oneformat #end if -#if str($param_param_default_optional_unrestricted_adv_snglformat): - -param_default_optional_unrestricted_adv_snglformat $param_param_default_optional_unrestricted_adv_snglformat +#if str($param_default_optional_oneformat): + -default_optional_oneformat $param_default_optional_oneformat #end if -#if str($param_param_wodefault_mandatory_unrestricted_multformat): - -param_wodefault_mandatory_unrestricted_multformat $param_param_wodefault_mandatory_unrestricted_multformat +#if str($param_wodefault_mandatory_multformat): + -wodefault_mandatory_multformat $param_wodefault_mandatory_multformat #end if -#if str($param_param_default_mandatory_unrestricted_multformat): - -param_default_mandatory_unrestricted_multformat $param_param_default_mandatory_unrestricted_multformat +#if str($param_default_mandatory_multformat): + -default_mandatory_multformat $param_default_mandatory_multformat #end if -#if str($param_param_wodefault_optional_unrestricted_multformat): - -param_wodefault_optional_unrestricted_multformat $param_param_wodefault_optional_unrestricted_multformat +#if str($param_wodefault_optional_multformat): + -wodefault_optional_multformat $param_wodefault_optional_multformat #end if -#if str($param_param_default_optional_unrestricted_multformat): - -param_default_optional_unrestricted_multformat $param_param_default_optional_unrestricted_multformat +#if str($param_default_optional_multformat): + -default_optional_multformat $param_default_optional_multformat #end if -#if str($param_param_wodefault_mandatory_unrestricted_adv_multformat): - -param_wodefault_mandatory_unrestricted_adv_multformat $param_param_wodefault_mandatory_unrestricted_adv_multformat + +#if $rep_param_list_mandatory_noformat: +-list_mandatory_noformat + #for token in $rep_param_list_mandatory_noformat: + #if " " in str(token): + "$token.param_list_mandatory_noformat" + #else + $token.param_list_mandatory_noformat + #end if + #end for +#end if + +#if $rep_param_list_optional_noformat: +-list_optional_noformat + #for token in $rep_param_list_optional_noformat: + #if " " in str(token): + "$token.param_list_optional_noformat" + #else + $token.param_list_optional_noformat + #end if + #end for +#end if + +#if $rep_param_list_mandatory_oneformat: +-list_mandatory_oneformat + #for token in $rep_param_list_mandatory_oneformat: + #if " " in str(token): + "$token.param_list_mandatory_oneformat" + #else + $token.param_list_mandatory_oneformat + #end if + #end for +#end if + +#if $rep_param_list_optional_oneformat: +-list_optional_oneformat + #for token in $rep_param_list_optional_oneformat: + #if " " in str(token): + "$token.param_list_optional_oneformat" + #else + $token.param_list_optional_oneformat + #end if + #end for +#end if + +#if $rep_param_list_mandatory_multformat: +-list_mandatory_multformat + #for token in $rep_param_list_mandatory_multformat: + #if " " in str(token): + "$token.param_list_mandatory_multformat" + #else + $token.param_list_mandatory_multformat + #end if + #end for +#end if + +#if $rep_param_list_optional_multformat: +-list_optional_multformat + #for token in $rep_param_list_optional_multformat: + #if " " in str(token): + "$token.param_list_optional_multformat" + #else + $token.param_list_optional_multformat + #end if + #end for +#end if +#if str($param_mandatory_noformat_adv): + -mandatory_noformat_adv $param_mandatory_noformat_adv +#end if +#if str($param_optional_noformat_adv): + -optional_noformat_adv $param_optional_noformat_adv +#end if +#if str($param_mandatory_oneformat_adv): + -mandatory_oneformat_adv $param_mandatory_oneformat_adv #end if -#if str($param_param_default_mandatory_unrestricted_adv_multformat): - -param_default_mandatory_unrestricted_adv_multformat $param_param_default_mandatory_unrestricted_adv_multformat +#if str($param_optional_oneformat_adv): + -optional_oneformat_adv $param_optional_oneformat_adv #end if -#if str($param_param_wodefault_optional_unrestricted_adv_multformat): - -param_wodefault_optional_unrestricted_adv_multformat $param_param_wodefault_optional_unrestricted_adv_multformat +#if str($param_mandatory_multformat_adv): + -mandatory_multformat_adv $param_mandatory_multformat_adv #end if -#if str($param_param_default_optional_unrestricted_adv_multformat): - -param_default_optional_unrestricted_adv_multformat $param_param_default_optional_unrestricted_adv_multformat +#if str($param_optional_multformat_adv): + -optional_multformat_adv $param_optional_multformat_adv #end if - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + Input File parameter tests. diff --git a/tests/test-data/repeat.ctd b/tests/test-data/repeat.ctd new file mode 100644 index 00000000..225db4c3 --- /dev/null +++ b/tests/test-data/repeat.ctd @@ -0,0 +1,125 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/repeat.xml b/tests/test-data/repeat.xml new file mode 100644 index 00000000..9134942e --- /dev/null +++ b/tests/test-data/repeat.xml @@ -0,0 +1,866 @@ + + + + + Repeat parameter tests + + echo RepeatTest + macros.xml + + + + + echo RepeatTest + + +#if $rep_param_string_wodefault_optional: +-string_wodefault_optional + #for token in $rep_param_string_wodefault_optional: + #if " " in str(token): + "$token.param_string_wodefault_optional" + #else + $token.param_string_wodefault_optional + #end if + #end for +#end if + +#if $rep_param_string_wodefault_mandatory: +-string_wodefault_mandatory + #for token in $rep_param_string_wodefault_mandatory: + #if " " in str(token): + "$token.param_string_wodefault_mandatory" + #else + $token.param_string_wodefault_mandatory + #end if + #end for +#end if + +#if $rep_param_string_default_optional: +-string_default_optional + #for token in $rep_param_string_default_optional: + #if " " in str(token): + "$token.param_string_default_optional" + #else + $token.param_string_default_optional + #end if + #end for +#end if + +#if $rep_param_string_default_mandatory: +-string_default_mandatory + #for token in $rep_param_string_default_mandatory: + #if " " in str(token): + "$token.param_string_default_mandatory" + #else + $token.param_string_default_mandatory + #end if + #end for +#end if + +#if $rep_param_int_wodefault_optional: +-int_wodefault_optional + #for token in $rep_param_int_wodefault_optional: + #if " " in str(token): + "$token.param_int_wodefault_optional" + #else + $token.param_int_wodefault_optional + #end if + #end for +#end if + +#if $rep_param_int_wodefault_mandatory: +-int_wodefault_mandatory + #for token in $rep_param_int_wodefault_mandatory: + #if " " in str(token): + "$token.param_int_wodefault_mandatory" + #else + $token.param_int_wodefault_mandatory + #end if + #end for +#end if + +#if $rep_param_int_default_optional: +-int_default_optional + #for token in $rep_param_int_default_optional: + #if " " in str(token): + "$token.param_int_default_optional" + #else + $token.param_int_default_optional + #end if + #end for +#end if + +#if $rep_param_int_default_mandatory: +-int_default_mandatory + #for token in $rep_param_int_default_mandatory: + #if " " in str(token): + "$token.param_int_default_mandatory" + #else + $token.param_int_default_mandatory + #end if + #end for +#end if + +#if $rep_param_int_resticted_wodefault_optional: +-int_resticted_wodefault_optional + #for token in $rep_param_int_resticted_wodefault_optional: + #if " " in str(token): + "$token.param_int_resticted_wodefault_optional" + #else + $token.param_int_resticted_wodefault_optional + #end if + #end for +#end if + +#if $rep_param_int_resticted_wodefault_mandatory: +-int_resticted_wodefault_mandatory + #for token in $rep_param_int_resticted_wodefault_mandatory: + #if " " in str(token): + "$token.param_int_resticted_wodefault_mandatory" + #else + $token.param_int_resticted_wodefault_mandatory + #end if + #end for +#end if + +#if $rep_param_int_resticted_default_optional: +-int_resticted_default_optional + #for token in $rep_param_int_resticted_default_optional: + #if " " in str(token): + "$token.param_int_resticted_default_optional" + #else + $token.param_int_resticted_default_optional + #end if + #end for +#end if + +#if $rep_param_int_resticted_default_mandatory: +-int_resticted_default_mandatory + #for token in $rep_param_int_resticted_default_mandatory: + #if " " in str(token): + "$token.param_int_resticted_default_mandatory" + #else + $token.param_int_resticted_default_mandatory + #end if + #end for +#end if + +#if $rep_param_double_wodefault_optional: +-double_wodefault_optional + #for token in $rep_param_double_wodefault_optional: + #if " " in str(token): + "$token.param_double_wodefault_optional" + #else + $token.param_double_wodefault_optional + #end if + #end for +#end if + +#if $rep_param_double_wodefault_mandatory: +-double_wodefault_mandatory + #for token in $rep_param_double_wodefault_mandatory: + #if " " in str(token): + "$token.param_double_wodefault_mandatory" + #else + $token.param_double_wodefault_mandatory + #end if + #end for +#end if + +#if $rep_param_double_default_optional: +-double_default_optional + #for token in $rep_param_double_default_optional: + #if " " in str(token): + "$token.param_double_default_optional" + #else + $token.param_double_default_optional + #end if + #end for +#end if + +#if $rep_param_double_default_mandatory: +-double_default_mandatory + #for token in $rep_param_double_default_mandatory: + #if " " in str(token): + "$token.param_double_default_mandatory" + #else + $token.param_double_default_mandatory + #end if + #end for +#end if + +#if $rep_param_double_resticted_wodefault_optional: +-double_resticted_wodefault_optional + #for token in $rep_param_double_resticted_wodefault_optional: + #if " " in str(token): + "$token.param_double_resticted_wodefault_optional" + #else + $token.param_double_resticted_wodefault_optional + #end if + #end for +#end if + +#if $rep_param_double_resticted_wodefault_mandatory: +-double_resticted_wodefault_mandatory + #for token in $rep_param_double_resticted_wodefault_mandatory: + #if " " in str(token): + "$token.param_double_resticted_wodefault_mandatory" + #else + $token.param_double_resticted_wodefault_mandatory + #end if + #end for +#end if + +#if $rep_param_double_resticted_default_optional: +-double_resticted_default_optional + #for token in $rep_param_double_resticted_default_optional: + #if " " in str(token): + "$token.param_double_resticted_default_optional" + #else + $token.param_double_resticted_default_optional + #end if + #end for +#end if + +#if $rep_param_double_resticted_default_mandatory: +-double_resticted_default_mandatory + #for token in $rep_param_double_resticted_default_mandatory: + #if " " in str(token): + "$token.param_double_resticted_default_mandatory" + #else + $token.param_double_resticted_default_mandatory + #end if + #end for +#end if + +#if $rep_param_string_wodefault_optional_adv: +-string_wodefault_optional_adv + #for token in $rep_param_string_wodefault_optional_adv: + #if " " in str(token): + "$token.param_string_wodefault_optional_adv" + #else + $token.param_string_wodefault_optional_adv + #end if + #end for +#end if + +#if $rep_param_string_wodefault_mandatory_adv: +-string_wodefault_mandatory_adv + #for token in $rep_param_string_wodefault_mandatory_adv: + #if " " in str(token): + "$token.param_string_wodefault_mandatory_adv" + #else + $token.param_string_wodefault_mandatory_adv + #end if + #end for +#end if + +#if $rep_param_string_default_optional_adv: +-string_default_optional_adv + #for token in $rep_param_string_default_optional_adv: + #if " " in str(token): + "$token.param_string_default_optional_adv" + #else + $token.param_string_default_optional_adv + #end if + #end for +#end if + +#if $rep_param_string_default_mandatory_adv: +-string_default_mandatory_adv + #for token in $rep_param_string_default_mandatory_adv: + #if " " in str(token): + "$token.param_string_default_mandatory_adv" + #else + $token.param_string_default_mandatory_adv + #end if + #end for +#end if + +#if $rep_param_int_wodefault_optional_adv: +-int_wodefault_optional_adv + #for token in $rep_param_int_wodefault_optional_adv: + #if " " in str(token): + "$token.param_int_wodefault_optional_adv" + #else + $token.param_int_wodefault_optional_adv + #end if + #end for +#end if + +#if $rep_param_int_wodefault_mandatory_adv: +-int_wodefault_mandatory_adv + #for token in $rep_param_int_wodefault_mandatory_adv: + #if " " in str(token): + "$token.param_int_wodefault_mandatory_adv" + #else + $token.param_int_wodefault_mandatory_adv + #end if + #end for +#end if + +#if $rep_param_int_default_optional_adv: +-int_default_optional_adv + #for token in $rep_param_int_default_optional_adv: + #if " " in str(token): + "$token.param_int_default_optional_adv" + #else + $token.param_int_default_optional_adv + #end if + #end for +#end if + +#if $rep_param_int_default_mandatory_adv: +-int_default_mandatory_adv + #for token in $rep_param_int_default_mandatory_adv: + #if " " in str(token): + "$token.param_int_default_mandatory_adv" + #else + $token.param_int_default_mandatory_adv + #end if + #end for +#end if + +#if $rep_param_int_resticted_wodefault_optional_adv: +-int_resticted_wodefault_optional_adv + #for token in $rep_param_int_resticted_wodefault_optional_adv: + #if " " in str(token): + "$token.param_int_resticted_wodefault_optional_adv" + #else + $token.param_int_resticted_wodefault_optional_adv + #end if + #end for +#end if + +#if $rep_param_int_resticted_wodefault_mandatory_adv: +-int_resticted_wodefault_mandatory_adv + #for token in $rep_param_int_resticted_wodefault_mandatory_adv: + #if " " in str(token): + "$token.param_int_resticted_wodefault_mandatory_adv" + #else + $token.param_int_resticted_wodefault_mandatory_adv + #end if + #end for +#end if + +#if $rep_param_int_resticted_default_optional_adv: +-int_resticted_default_optional_adv + #for token in $rep_param_int_resticted_default_optional_adv: + #if " " in str(token): + "$token.param_int_resticted_default_optional_adv" + #else + $token.param_int_resticted_default_optional_adv + #end if + #end for +#end if + +#if $rep_param_int_resticted_default_mandatory_adv: +-int_resticted_default_mandatory_adv + #for token in $rep_param_int_resticted_default_mandatory_adv: + #if " " in str(token): + "$token.param_int_resticted_default_mandatory_adv" + #else + $token.param_int_resticted_default_mandatory_adv + #end if + #end for +#end if + +#if $rep_param_double_wodefault_optional_adv: +-double_wodefault_optional_adv + #for token in $rep_param_double_wodefault_optional_adv: + #if " " in str(token): + "$token.param_double_wodefault_optional_adv" + #else + $token.param_double_wodefault_optional_adv + #end if + #end for +#end if + +#if $rep_param_double_wodefault_mandatory_adv: +-double_wodefault_mandatory_adv + #for token in $rep_param_double_wodefault_mandatory_adv: + #if " " in str(token): + "$token.param_double_wodefault_mandatory_adv" + #else + $token.param_double_wodefault_mandatory_adv + #end if + #end for +#end if + +#if $rep_param_double_default_optional_adv: +-double_default_optional_adv + #for token in $rep_param_double_default_optional_adv: + #if " " in str(token): + "$token.param_double_default_optional_adv" + #else + $token.param_double_default_optional_adv + #end if + #end for +#end if + +#if $rep_param_double_default_mandatory_adv: +-double_default_mandatory_adv + #for token in $rep_param_double_default_mandatory_adv: + #if " " in str(token): + "$token.param_double_default_mandatory_adv" + #else + $token.param_double_default_mandatory_adv + #end if + #end for +#end if + +#if $rep_param_double_resticted_wodefault_optional_adv: +-double_resticted_wodefault_optional_adv + #for token in $rep_param_double_resticted_wodefault_optional_adv: + #if " " in str(token): + "$token.param_double_resticted_wodefault_optional_adv" + #else + $token.param_double_resticted_wodefault_optional_adv + #end if + #end for +#end if + +#if $rep_param_double_resticted_wodefault_mandatory_adv: +-double_resticted_wodefault_mandatory_adv + #for token in $rep_param_double_resticted_wodefault_mandatory_adv: + #if " " in str(token): + "$token.param_double_resticted_wodefault_mandatory_adv" + #else + $token.param_double_resticted_wodefault_mandatory_adv + #end if + #end for +#end if + +#if $rep_param_double_resticted_default_optional_adv: +-double_resticted_default_optional_adv + #for token in $rep_param_double_resticted_default_optional_adv: + #if " " in str(token): + "$token.param_double_resticted_default_optional_adv" + #else + $token.param_double_resticted_default_optional_adv + #end if + #end for +#end if + +#if $rep_param_double_resticted_default_mandatory_adv: +-double_resticted_default_mandatory_adv + #for token in $rep_param_double_resticted_default_mandatory_adv: + #if " " in str(token): + "$token.param_double_resticted_default_mandatory_adv" + #else + $token.param_double_resticted_default_mandatory_adv + #end if + #end for +#end if +> $param_stdout + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Repeat parameter tests. + + +For more information, visit http://docs.are/unavailable.html + diff --git a/tests/test-data/select.ctd b/tests/test-data/select.ctd index f141dd12..77048022 100644 --- a/tests/test-data/select.ctd +++ b/tests/test-data/select.ctd @@ -1,19 +1,44 @@ - - - - + + + + - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test-data/select.xml b/tests/test-data/select.xml index 437c68ba..7e243ccd 100644 --- a/tests/test-data/select.xml +++ b/tests/test-data/select.xml @@ -2,7 +2,7 @@ - String parameter tests + Select parameter tests echo SelectTest macros.xml @@ -12,112 +12,256 @@ echo SelectTest -#if $param_param_wodefault_mandatory_restricted: - -param_wodefault_mandatory_restricted - #if " " in str($param_param_wodefault_mandatory_restricted): - "$param_param_wodefault_mandatory_restricted" +#if $param_wodefault_mandatory: + -wodefault_mandatory + #if " " in str($param_wodefault_mandatory): + "$param_wodefault_mandatory" #else - $param_param_wodefault_mandatory_restricted + $param_wodefault_mandatory #end if #end if -#if $param_param_default_mandatory_restricted: - -param_default_mandatory_restricted - #if " " in str($param_param_default_mandatory_restricted): - "$param_param_default_mandatory_restricted" +#if $param_default_mandatory: + -default_mandatory + #if " " in str($param_default_mandatory): + "$param_default_mandatory" #else - $param_param_default_mandatory_restricted + $param_default_mandatory #end if #end if -#if $param_param_wodefault_optional_restricted: - -param_wodefault_optional_restricted - #if " " in str($param_param_wodefault_optional_restricted): - "$param_param_wodefault_optional_restricted" +#if $param_wodefault_optional: + -wodefault_optional + #if " " in str($param_wodefault_optional): + "$param_wodefault_optional" #else - $param_param_wodefault_optional_restricted + $param_wodefault_optional #end if #end if -#if $param_param_default_optional_restricted: - -param_default_optional_restricted - #if " " in str($param_param_default_optional_restricted): - "$param_param_default_optional_restricted" +#if $param_default_optional: + -default_optional + #if " " in str($param_default_optional): + "$param_default_optional" #else - $param_param_default_optional_restricted + $param_default_optional #end if #end if + +#if $rep_param_list_wodefault_optional: +-list_wodefault_optional + #for token in $rep_param_list_wodefault_optional: + #if " " in str(token): + "$token.param_list_wodefault_optional" + #else + $token.param_list_wodefault_optional + #end if + #end for +#end if + +#if $rep_param_list_wodefault_mandatory: +-list_wodefault_mandatory + #for token in $rep_param_list_wodefault_mandatory: + #if " " in str(token): + "$token.param_list_wodefault_mandatory" + #else + $token.param_list_wodefault_mandatory + #end if + #end for +#end if + +#if $rep_param_list_default_optional: +-list_default_optional + #for token in $rep_param_list_default_optional: + #if " " in str(token): + "$token.param_list_default_optional" + #else + $token.param_list_default_optional + #end if + #end for +#end if + +#if $rep_param_list_default_mandatory: +-list_default_mandatory + #for token in $rep_param_list_default_mandatory: + #if " " in str(token): + "$token.param_list_default_mandatory" + #else + $token.param_list_default_mandatory + #end if + #end for +#end if + +#if $rep_param_list_wodefault_optional_adv: +-list_wodefault_optional_adv + #for token in $rep_param_list_wodefault_optional_adv: + #if " " in str(token): + "$token.param_list_wodefault_optional_adv" + #else + $token.param_list_wodefault_optional_adv + #end if + #end for +#end if + +#if $rep_param_list_wodefault_mandatory_adv: +-list_wodefault_mandatory_adv + #for token in $rep_param_list_wodefault_mandatory_adv: + #if " " in str(token): + "$token.param_list_wodefault_mandatory_adv" + #else + $token.param_list_wodefault_mandatory_adv + #end if + #end for +#end if + +#if $rep_param_list_default_optional_adv: +-list_default_optional_adv + #for token in $rep_param_list_default_optional_adv: + #if " " in str(token): + "$token.param_list_default_optional_adv" + #else + $token.param_list_default_optional_adv + #end if + #end for +#end if + +#if $rep_param_list_default_mandatory_adv: +-list_default_mandatory_adv + #for token in $rep_param_list_default_mandatory_adv: + #if " " in str(token): + "$token.param_list_default_mandatory_adv" + #else + $token.param_list_default_mandatory_adv + #end if + #end for +#end if #if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_param_wodefault_mandatory_restricted_adv: - -param_wodefault_mandatory_restricted_adv - #if " " in str($adv_opts.param_param_wodefault_mandatory_restricted_adv): - "$adv_opts.param_param_wodefault_mandatory_restricted_adv" + #if $adv_opts.param_wodefault_mandatory_adv: + -wodefault_mandatory_adv + #if " " in str($adv_opts.param_wodefault_mandatory_adv): + "$adv_opts.param_wodefault_mandatory_adv" #else - $adv_opts.param_param_wodefault_mandatory_restricted_adv + $adv_opts.param_wodefault_mandatory_adv #end if #end if - #if $adv_opts.param_param_default_mandatory_restricted_adv: - -param_default_mandatory_restricted_adv - #if " " in str($adv_opts.param_param_default_mandatory_restricted_adv): - "$adv_opts.param_param_default_mandatory_restricted_adv" + #if $adv_opts.param_default_mandatory_adv: + -default_mandatory_adv + #if " " in str($adv_opts.param_default_mandatory_adv): + "$adv_opts.param_default_mandatory_adv" #else - $adv_opts.param_param_default_mandatory_restricted_adv + $adv_opts.param_default_mandatory_adv #end if #end if - #if $adv_opts.param_param_wodefault_optional_restricted_adv: - -param_wodefault_optional_restricted_adv - #if " " in str($adv_opts.param_param_wodefault_optional_restricted_adv): - "$adv_opts.param_param_wodefault_optional_restricted_adv" + #if $adv_opts.param_wodefault_optional_adv: + -wodefault_optional_adv + #if " " in str($adv_opts.param_wodefault_optional_adv): + "$adv_opts.param_wodefault_optional_adv" #else - $adv_opts.param_param_wodefault_optional_restricted_adv + $adv_opts.param_wodefault_optional_adv #end if #end if - #if $adv_opts.param_param_default_optional_restricted_adv: - -param_default_optional_restricted_adv - #if " " in str($adv_opts.param_param_default_optional_restricted_adv): - "$adv_opts.param_param_default_optional_restricted_adv" + #if $adv_opts.param_default_optional_adv: + -default_optional_adv + #if " " in str($adv_opts.param_default_optional_adv): + "$adv_opts.param_default_optional_adv" #else - $adv_opts.param_param_default_optional_restricted_adv + $adv_opts.param_default_optional_adv #end if #end if #end if > $param_stdout - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + @@ -127,7 +271,7 @@ - String parameter tests. + Select parameter tests. For more information, visit http://docs.are/unavailable.html diff --git a/tests/test-data/string.ctd b/tests/test-data/string.ctd index 11517f36..5c0e5fc7 100644 --- a/tests/test-data/string.ctd +++ b/tests/test-data/string.ctd @@ -2,7 +2,7 @@ - + diff --git a/tests/test_galaxy_cli.py b/tests/test_galaxy_cli.py index 51de457a..9659931f 100644 --- a/tests/test_galaxy_cli.py +++ b/tests/test_galaxy_cli.py @@ -16,12 +16,13 @@ class GalaxyCliTestCase(unittest.TestCase): def _compare_cli_output(self, fileprefix): in_pth = to_test_data('{}.ctd'.format(fileprefix)) macro_pth = to_test_data('macros.xml') + ftypes_pth = to_test_data('filetypes.txt') tmp = tempfile.mkdtemp() out_file = os.path.join(tmp, '{}.xml'.format(fileprefix)) #out_file = to_test_data('{}.xml'.format(fileprefix)) - cmd = ['CTDConverter', 'galaxy', '-i', in_pth, '-o', out_file, '-m', macro_pth, '-b', 'version'] + cmd = ['CTDConverter', 'galaxy', '-i', in_pth, '-o', out_file, '-f', ftypes_pth, '-m', macro_pth, '-b', 'version'] print(cmd) popen = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) From 270bd113db71168bd441f0b49ad75b77ebec9abc Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 16 Jul 2019 15:31:26 +0200 Subject: [PATCH 09/11] added filetypes.txt --- tests/test-data/filetypes.txt | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 tests/test-data/filetypes.txt diff --git a/tests/test-data/filetypes.txt b/tests/test-data/filetypes.txt new file mode 100644 index 00000000..ae3d61a2 --- /dev/null +++ b/tests/test-data/filetypes.txt @@ -0,0 +1,4 @@ +# CTD type # Galaxy type # Long Galaxy data type # Mimetype +ext txt galaxy.datatypes.data:Text +eyt txt galaxy.datatypes.data:Text +ezt txt galaxy.datatypes.data:Text From 57541bc05d5e4034509339bf976963c90c7e6ffe Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 16 Jul 2019 16:06:03 +0200 Subject: [PATCH 10/11] advanced repeats were not advanced --- tests/test-data/repeat.ctd | 40 ++-- tests/test-data/repeat.xml | 444 +++++++++++++++++++------------------ 2 files changed, 244 insertions(+), 240 deletions(-) diff --git a/tests/test-data/repeat.ctd b/tests/test-data/repeat.ctd index 225db4c3..75d90af5 100644 --- a/tests/test-data/repeat.ctd +++ b/tests/test-data/repeat.ctd @@ -63,58 +63,58 @@ - - - + + + - + - - - + + + - + - - - + + + - + - - - + + + - + - - - + + + - + diff --git a/tests/test-data/repeat.xml b/tests/test-data/repeat.xml index 9134942e..028177a3 100644 --- a/tests/test-data/repeat.xml +++ b/tests/test-data/repeat.xml @@ -232,7 +232,8 @@ #end if #end for #end if - +#if $adv_opts.adv_opts_selector=='advanced': + #if $rep_param_string_wodefault_optional_adv: -string_wodefault_optional_adv #for token in $rep_param_string_wodefault_optional_adv: @@ -243,7 +244,7 @@ #end if #end for #end if - + #if $rep_param_string_wodefault_mandatory_adv: -string_wodefault_mandatory_adv #for token in $rep_param_string_wodefault_mandatory_adv: @@ -254,7 +255,7 @@ #end if #end for #end if - + #if $rep_param_string_default_optional_adv: -string_default_optional_adv #for token in $rep_param_string_default_optional_adv: @@ -265,7 +266,7 @@ #end if #end for #end if - + #if $rep_param_string_default_mandatory_adv: -string_default_mandatory_adv #for token in $rep_param_string_default_mandatory_adv: @@ -276,7 +277,7 @@ #end if #end for #end if - + #if $rep_param_int_wodefault_optional_adv: -int_wodefault_optional_adv #for token in $rep_param_int_wodefault_optional_adv: @@ -287,7 +288,7 @@ #end if #end for #end if - + #if $rep_param_int_wodefault_mandatory_adv: -int_wodefault_mandatory_adv #for token in $rep_param_int_wodefault_mandatory_adv: @@ -298,7 +299,7 @@ #end if #end for #end if - + #if $rep_param_int_default_optional_adv: -int_default_optional_adv #for token in $rep_param_int_default_optional_adv: @@ -309,7 +310,7 @@ #end if #end for #end if - + #if $rep_param_int_default_mandatory_adv: -int_default_mandatory_adv #for token in $rep_param_int_default_mandatory_adv: @@ -320,7 +321,7 @@ #end if #end for #end if - + #if $rep_param_int_resticted_wodefault_optional_adv: -int_resticted_wodefault_optional_adv #for token in $rep_param_int_resticted_wodefault_optional_adv: @@ -331,7 +332,7 @@ #end if #end for #end if - + #if $rep_param_int_resticted_wodefault_mandatory_adv: -int_resticted_wodefault_mandatory_adv #for token in $rep_param_int_resticted_wodefault_mandatory_adv: @@ -342,7 +343,7 @@ #end if #end for #end if - + #if $rep_param_int_resticted_default_optional_adv: -int_resticted_default_optional_adv #for token in $rep_param_int_resticted_default_optional_adv: @@ -353,7 +354,7 @@ #end if #end for #end if - + #if $rep_param_int_resticted_default_mandatory_adv: -int_resticted_default_mandatory_adv #for token in $rep_param_int_resticted_default_mandatory_adv: @@ -364,7 +365,7 @@ #end if #end for #end if - + #if $rep_param_double_wodefault_optional_adv: -double_wodefault_optional_adv #for token in $rep_param_double_wodefault_optional_adv: @@ -375,7 +376,7 @@ #end if #end for #end if - + #if $rep_param_double_wodefault_mandatory_adv: -double_wodefault_mandatory_adv #for token in $rep_param_double_wodefault_mandatory_adv: @@ -386,7 +387,7 @@ #end if #end for #end if - + #if $rep_param_double_default_optional_adv: -double_default_optional_adv #for token in $rep_param_double_default_optional_adv: @@ -397,7 +398,7 @@ #end if #end for #end if - + #if $rep_param_double_default_mandatory_adv: -double_default_mandatory_adv #for token in $rep_param_double_default_mandatory_adv: @@ -408,7 +409,7 @@ #end if #end for #end if - + #if $rep_param_double_resticted_wodefault_optional_adv: -double_resticted_wodefault_optional_adv #for token in $rep_param_double_resticted_wodefault_optional_adv: @@ -419,7 +420,7 @@ #end if #end for #end if - + #if $rep_param_double_resticted_wodefault_mandatory_adv: -double_resticted_wodefault_mandatory_adv #for token in $rep_param_double_resticted_wodefault_mandatory_adv: @@ -430,7 +431,7 @@ #end if #end for #end if - + #if $rep_param_double_resticted_default_optional_adv: -double_resticted_default_optional_adv #for token in $rep_param_double_resticted_default_optional_adv: @@ -441,7 +442,7 @@ #end if #end for #end if - + #if $rep_param_double_resticted_default_mandatory_adv: -double_resticted_default_mandatory_adv #for token in $rep_param_double_resticted_default_mandatory_adv: @@ -452,6 +453,7 @@ #end if #end for #end if +#end if > $param_stdout @@ -655,206 +657,208 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 79cc8cf27b625f073926e7d2a98cca47f5c9e47f Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 16 Jul 2019 16:14:59 +0200 Subject: [PATCH 11/11] add missing tests --- tests/test_galaxy_cli.py | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/tests/test_galaxy_cli.py b/tests/test_galaxy_cli.py index 9659931f..d87c9ede 100644 --- a/tests/test_galaxy_cli.py +++ b/tests/test_galaxy_cli.py @@ -41,8 +41,8 @@ def _compare_cli_output(self, fileprefix): for i in range(0, len(new_l)): self.assertEqual(new_l[i].rstrip(), old_l[i].rstrip()) - def test_galaxy_cli_full_file_ctd(self): - self._compare_cli_output('AccurateMassSearch') + def test_galaxy_cli_bool_ctd(self): + self._compare_cli_output('bool') def test_galaxy_cli_empty_ctd(self): self._compare_cli_output('empty') @@ -53,12 +53,20 @@ def test_galaxy_cli_float_ctd(self): def test_galaxy_cli_integer_ctd(self): self._compare_cli_output('integer') + def test_galaxy_cli_repeat_ctd(self): + self._compare_cli_output('repeat') + def test_galaxy_cli_select_ctd(self): self._compare_cli_output('select') def test_galaxy_cli_string_ctd(self): self._compare_cli_output('string') + def test_galaxy_cli_ifile_ctd(self): + self._compare_cli_output('ifile') + + def test_galaxy_cli_ofile_ctd(self): + self._compare_cli_output('ofile') if __name__ == '__main__':