WorkflowConversion · bernt-matthias · Jul 6, 2019 · Jul 9, 2019 · Jul 15, 2019 · Jul 15, 2019
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,42 @@
+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
+  - 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
+  - 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
diff --git a/tests/test-data/bool.ctd b/tests/test-data/bool.ctd
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool ctdVersion="1.7" version="2.3.0" name="echo BoolTest" docurl="http://docs.are/unavailable.html" category="Bool Test" >
+<description><![CDATA[Bool parameter tests]]></description>
+<manual><![CDATA[Bool parameter tests.]]></manual>
+<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <NODE name="BoolTest" description="Bool test.">
+    <ITEM name="version" value="2.3.0" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
+    <NODE name="1" description="Instance &apos;1&apos; section for &apos;BoolTest&apos;">
+      <!-- note bool parameters seem to be always required false -->
+      <ITEM name="true_optional_unrestricted"      value="true"  type="string" description="bool" required="false" advanced="false" restrictions="true,false"/>
+      <ITEM name="false_optional_unrestricted"     value="false" type="string" description="bool" required="false" advanced="false" restrictions="true,false"/>
+      <ITEM name="true_optional_unrestricted_adv"  value="true"  type="string" description="bool" required="false" advanced="true"  restrictions="true,false"/>
+      <ITEM name="false_optional_unrestricted_adv" value="false" type="string" description="bool" required="false" advanced="true"  restrictions="true,false"/>
+    </NODE>
+  </NODE>
+</PARAMETERS>
+</tool>
diff --git a/tests/test-data/bool.xml b/tests/test-data/bool.xml
@@ -0,0 +1,62 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
+<!--Proposed Tool Section: [Bool Test]-->
+<tool id="echo BoolTest" name="echo BoolTest" version="2.3.0">
+  <description>Bool parameter tests</description>
+  <macros>
+    <token name="@EXECUTABLE@">echo BoolTest</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <expand macro="references"/>
+  <command>echo BoolTest
+
+#if $param_true_optional_unrestricted:
+  -true_optional_unrestricted
+  #if " " in str($param_true_optional_unrestricted):
+    "$param_true_optional_unrestricted"
+  #else
+    $param_true_optional_unrestricted
+  #end if
+#end if
+#if $param_false_optional_unrestricted:
+  -false_optional_unrestricted
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #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_true_optional_unrestricted_adv
+  #end if
+#end if
+    #if $adv_opts.param_false_optional_unrestricted_adv:
+  -false_optional_unrestricted_adv
+#end if
+#end if
+&gt; $param_stdout
+</command>
+  <inputs>
+    <param name="param_true_optional_unrestricted" display="radio" type="select" optional="False" value="true" label="bool" help="(-true_optional_unrestricted) ">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <param name="param_false_optional_unrestricted" display="radio" type="boolean" truevalue="-false_optional_unrestricted" falsevalue="" checked="false" optional="True" label="bool" help="(-false_optional_unrestricted) "/>
+    <expand macro="advanced_options">
+      <param name="param_true_optional_unrestricted_adv" display="radio" type="select" optional="False" value="true" label="bool" help="(-true_optional_unrestricted_adv) ">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_false_optional_unrestricted_adv" display="radio" type="boolean" truevalue="-false_optional_unrestricted_adv" falsevalue="" checked="false" optional="True" label="bool" help="(-false_optional_unrestricted_adv) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_stdout" format="txt" label="Output from stdout"/>
+  </outputs>
+  <help>Bool parameter tests.
+
+
+For more information, visit http://docs.are/unavailable.html</help>
+</tool>
diff --git a/tests/test-data/empty.ctd b/tests/test-data/empty.ctd
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool ctdVersion="1.7" version="2.3.0" name="echo StringTest" docurl="http://docs.are/unavailable.html" category="String Test" >
+<description><![CDATA[String parameter tests]]></description>
+<manual><![CDATA[String parameter tests.]]></manual>
+<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <NODE name="StringTest" description="String test.">
+    <ITEM name="version" value="2.3.0" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
+    <NODE name="1" description="Instance &apos;1&apos; section for &apos;StringTest&apos;">
+    </NODE>
+  </NODE>
+</PARAMETERS>
+</tool>
diff --git a/tests/test-data/empty.xml b/tests/test-data/empty.xml
@@ -0,0 +1,25 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
+<!--Proposed Tool Section: [String Test]-->
+<tool id="echo StringTest" name="echo StringTest" version="2.3.0">
+  <description>String parameter tests</description>
+  <macros>
+    <token name="@EXECUTABLE@">echo StringTest</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <expand macro="references"/>
+  <command>echo StringTest
+
+&gt; $param_stdout
+</command>
+  <inputs/>
+  <outputs>
+    <data name="param_stdout" format="txt" label="Output from stdout"/>
+  </outputs>
+  <help>String parameter tests.
+
+
+For more information, visit http://docs.are/unavailable.html</help>
+</tool>
diff --git a/tests/test-data/filetypes.txt 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
diff --git a/tests/test-data/float.ctd b/tests/test-data/float.ctd
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool ctdVersion="1.7" version="2.3.0" name="echo FloatTest" docurl="http://docs.are/unavailable.html" category="String Test" >
+<description><![CDATA[Floateger parameter tests]]></description>
+<manual><![CDATA[Floateger parameter tests.]]></manual>
+<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <NODE name="FloategerTest" description="Float test.">
+    <ITEM name="version" value="2.3.0" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
+    <NODE name="1" description="Instance &apos;1&apos; section for &apos;FloategerTest&apos;">
+      <ITEM name="param_wodefault_mandatory_unrestricted"     value=""    type="double" description="float" required="true"  advanced="false" />
+      <ITEM name="param_default_mandatory_unrestricted"       value="0.0" type="double" description="float" required="true"  advanced="false" />
+      <ITEM name="param_wodefault_optional_unrestricted"      value=""    type="double" description="float" required="false" advanced="false" />
+      <ITEM name="param_default_optional_unrestricted"        value="0.0" type="double" description="float" required="false" advanced="false" />
+      <ITEM name="param_wodefault_mandatory_unrestricted_adv" value=""    type="double" description="float" required="true"  advanced="true" />
+      <ITEM name="param_default_mandatory_unrestricted_adv"   value="0.0" type="double" description="float" required="true"  advanced="true" />
+      <ITEM name="param_wodefault_optional_unrestricted_adv"  value=""    type="double" description="float" required="false" advanced="true" />
+      <ITEM name="param_default_optional_unrestricted_adv"    value="0.0" type="double" description="float" required="false" advanced="true" />
+
+      <ITEM name="param_wodefault_mandatory_unrestricted_min"     value=""    type="double" description="float" required="true"  advanced="false" restrictions="0.0:"/>
+      <ITEM name="param_default_mandatory_unrestricted_min"       value="0.0" type="double" description="float" required="true"  advanced="false" restrictions="0.0:"/>
+      <ITEM name="param_wodefault_optional_unrestricted_min"      value=""    type="double" description="float" required="false" advanced="false" restrictions="0.0:"/>
+      <ITEM name="param_default_optional_unrestricted_min"        value="0.0" type="double" description="float" required="false" advanced="false" restrictions="0.0:"/>
+      <ITEM name="param_wodefault_mandatory_unrestricted_adv_min" value=""    type="double" description="float" required="true"  advanced="true" restrictions="0.0:"/>
+      <ITEM name="param_default_mandatory_unrestricted_adv_min"   value="0.0" type="double" description="float" required="true"  advanced="true" restrictions="0.0:"/>
+      <ITEM name="param_wodefault_optional_unrestricted_adv_min"  value=""    type="double" description="float" required="false" advanced="true" restrictions="0.0:"/>
+      <ITEM name="param_default_optional_unrestricted_adv_min"    value="0.0" type="double" description="float" required="false" advanced="true" restrictions="0.0:"/>
+
+      <ITEM name="param_wodefault_mandatory_unrestricted_max"     value=""    type="double" description="float" required="true"  advanced="false" restrictions=":100.0"/>
+      <ITEM name="param_default_mandatory_unrestricted_max"       value="0.0" type="double" description="float" required="true"  advanced="false" restrictions=":100.0"/>
+      <ITEM name="param_wodefault_optional_unrestricted_max"      value=""    type="double" description="float" required="false" advanced="false" restrictions=":100.0"/>
+      <ITEM name="param_default_optional_unrestricted_max"        value="0.0" type="double" description="float" required="false" advanced="false" restrictions=":100.0"/>
+      <ITEM name="param_wodefault_mandatory_unrestricted_adv_max" value=""    type="double" description="float" required="true"  advanced="true" restrictions=":100.0"/>
+      <ITEM name="param_default_mandatory_unrestricted_adv_max"   value="0.0" type="double" description="float" required="true"  advanced="true" restrictions=":100.0"/>
+      <ITEM name="param_wodefault_optional_unrestricted_adv_max"  value=""    type="double" description="float" required="false" advanced="true" restrictions=":100.0"/>
+      <ITEM name="param_default_optional_unrestricted_adv_max"    value="0.0" type="double" description="float" required="false" advanced="true" restrictions=":100.0"/>
+
+      <ITEM name="param_wodefault_mandatory_unrestricted_minmax"     value=""    type="double" description="float" required="true"  advanced="false" restrictions="0.0:100.0"/>
+      <ITEM name="param_default_mandatory_unrestricted_minmax"       value="0.0" type="double" description="float" required="true"  advanced="false" restrictions="0.0:100.0"/>
+      <ITEM name="param_wodefault_optional_unrestricted_minmax"      value=""    type="double" description="float" required="false" advanced="false" restrictions="0.0:100.0"/>
+      <ITEM name="param_default_optional_unrestricted_minmax"        value="0.0" type="double" description="float" required="false" advanced="false" restrictions="0.0:100.0"/>
+      <ITEM name="param_wodefault_mandatory_unrestricted_adv_minmax" value=""    type="double" description="float" required="true"  advanced="true" restrictions="0.0:100.0"/>
+      <ITEM name="param_default_mandatory_unrestricted_adv_minmax"   value="0.0" type="double" description="float" required="true"  advanced="true" restrictions="0.0:100.0"/>
+      <ITEM name="param_wodefault_optional_unrestricted_adv_minmax"  value=""    type="double" description="float" required="false" advanced="true" restrictions="0.0:100.0"/>
+      <ITEM name="param_default_optional_unrestricted_adv_minmax"    value="0.0" type="double" description="float" required="false" advanced="true" restrictions="0.0:100.0"/>
+    </NODE>
+  </NODE>
+</PARAMETERS>
+</tool>