add unit tests

.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

tests/test-data/AccurateMassSearch.ctd

@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool ctdVersion="1.7" version="2.4.0-HEAD-2018-10-26" name="AccurateMassSearch" docurl="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html" category="Utilities" >
+<description><![CDATA[Match MS signals to molecules from a database by mass.]]></description>
+<manual><![CDATA[Match MS signals to molecules from a database by mass.]]></manual>
+<citations>
+  <citation doi="10.1038/nmeth.3959" url="" />
+</citations>
+<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="AccurateMassSearch" description="Match MS signals to molecules from a database by mass.">
+    <ITEM name="version" value="2.4.0-HEAD-2018-10-26" 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;AccurateMassSearch&apos;">
+      <ITEM name="in" value="" type="input-file" description="featureXML or consensusXML file" required="true" advanced="false" supported_formats="*.featureXML,*.consensusXML" />
+      <ITEM name="out" value="" type="output-file" description="mzTab file" required="true" advanced="false" supported_formats="*.mzTab" />
+      <ITEM name="out_annotation" value="" type="output-file" description="A copy of the input file, annotated with matching hits from the database." required="false" advanced="false" supported_formats="*.featureXML,*.consensusXML" />
+      <ITEM name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" type="input-file" description="This file contains the list of potential positive adducts that will be looked for in the database. Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the default will be used." required="true" advanced="false" supported_formats="*.tsv" />
+      <ITEM name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" type="input-file" description="This file contains the list of potential negative adducts that will be looked for in the database. Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the default will be used." required="true" advanced="false" supported_formats="*.tsv" />
+      <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
+      <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
+      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
+      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
+      <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
+      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
+      <NODE name="db" description="Database files which contain the identifications">
+        <ITEMLIST name="mapping" type="input-file" description="Database input file(s), containing three tab-separated columns of mass, formula, identifier. If &apos;mass&apos; is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used." required="true" advanced="false" supported_formats="*.tsv">
+          <LISTITEM value="CHEMISTRY/HMDBMappingFile.tsv"/>
+        </ITEMLIST>
+        <ITEMLIST name="struct" type="input-file" description="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file. SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used." required="true" advanced="false" supported_formats="*.tsv">
+          <LISTITEM value="CHEMISTRY/HMDB2StructMapping.tsv"/>
+        </ITEMLIST>
+      </NODE>
+      <NODE name="algorithm" description="Algorithm parameters section">
+        <ITEM name="mass_error_value" value="5" type="double" description="Tolerance allowed for accurate mass search." required="false" advanced="false" />
+        <ITEM name="mass_error_unit" value="ppm" type="string" description="Unit of mass error (ppm or Da)" required="false" advanced="false" restrictions="ppm,Da" />
+        <ITEM name="ionization_mode" value="positive" type="string" description="Positive or negative ionization mode? If &apos;auto&apos; is used, the first feature of the input map must contain the meta-value &apos;scan_polarity&apos;. If its missing, the tool will exit with error." required="false" advanced="false" restrictions="positive,negative,auto" />
+        <ITEM name="isotopic_similarity" value="false" type="string" description="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)." required="false" advanced="false" restrictions="false,true" />
+        <ITEM name="keep_unidentified_masses" value="false" type="string" description="Keep features that did not yield any DB hit." required="false" advanced="false" restrictions="false,true" />
+        <NODE name="mzTab" description="">
+          <ITEM name="exportIsotopeIntensities" value="0" type="int" description="[featureXML input only] Number of extra columns in mzTab output, which provide intensities up to the x&apos;th isotope. &apos;0&apos; to deactivate, &apos;1&apos; for monoisotopic peak, etc. If a feature does not have a certain isotope, &apos;null&apos; will be reported." required="false" advanced="false" restrictions="0:" />
+        </NODE>
+      </NODE>
+    </NODE>
+  </NODE>
+</PARAMETERS>
+</tool>

tests/test-data/AccurateMassSearch.xml

@@ -0,0 +1,144 @@
+<?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: [Utilities]-->
+<tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.4.0-HEAD-2018-10-26">
+  <description>Match MS signals to molecules from a database by mass.</description>
+  <macros>
+    <token name="@EXECUTABLE@">AccurateMassSearch</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <expand macro="references"/>
+  <command>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
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" label="featureXML or consensusXML file" help="(-in) "/>
+    <param name="param_positive_adducts" type="data" format="tsv" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database" help="(-positive_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
+    <param name="param_negative_adducts" type="data" format="tsv" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database" help="(-negative_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
+    <param name="param_threads" type="integer" value="1" label="Sets the number of threads allowed to be used by the TOPP tool" help="(-threads) "/>
+    <param name="param_db_mapping" type="data" format="tsv" multiple="true" optional="False" size="30" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="(-mapping) If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_db_struct" type="data" format="tsv" multiple="true" optional="False" size="30" value="CHEMISTRY/HMDB2StructMapping.tsv" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="(-struct) SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_algorithm_mass_error_value" type="float" value="5.0" label="Tolerance allowed for accurate mass search" help="(-mass_error_value) "/>
+    <param name="param_algorithm_mass_error_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) ">
+      <option value="ppm" selected="true">ppm</option>
+      <option value="Da">Da</option>
+    </param>
+    <param name="param_algorithm_ionization_mode" display="radio" type="select" optional="False" value="positive" label="Positive or negative ionization mode?" help="(-ionization_mode) If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
+      <option value="positive" selected="true">positive</option>
+      <option value="negative">negative</option>
+      <option value="auto">auto</option>
+    </param>
+    <param name="param_algorithm_isotopic_similarity" display="radio" type="boolean" truevalue="-algorithm:isotopic_similarity" falsevalue="" checked="false" optional="True" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" help="(-isotopic_similarity) "/>
+    <param name="param_algorithm_keep_unidentified_masses" display="radio" type="boolean" truevalue="-algorithm:keep_unidentified_masses" falsevalue="" checked="false" optional="True" label="Keep features that did not yield any DB hit" help="(-keep_unidentified_masses) "/>
+    <param name="param_algorithm_mzTab_exportIsotopeIntensities" type="integer" min="0" optional="True" value="0" label="[featureXML input only] Number of extra columns in mzTab output, which provide intensities up to the x'th isotope" help="(-exportIsotopeIntensities) '0' to deactivate, '1' for monoisotopic peak, etc. If a feature does not have a certain isotope, 'null' will be reported"/>
+    <expand macro="advanced_options">
+      <param name="param_log" type="text" size="30" label="Name of log file (created only when specified)" help="(-log) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_debug" type="integer" value="0" label="Sets the debug level" help="(-debug) "/>
+      <param name="param_no_progress" display="radio" type="boolean" truevalue="-no_progress" falsevalue="" checked="false" optional="True" label="Disables progress logging to command line" help="(-no_progress) "/>
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_test" display="radio" type="boolean" truevalue="-test" falsevalue="" checked="false" optional="True" label="Enables the test mode (needed for internal use only)" help="(-test) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="mzTab"/>
+    <data name="param_out_annotation" label="${tool.name} on ${on_string}: annotation" format="featureXML,consensusXML"/>
+  </outputs>
+  <help>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</help>
+</tool>

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="http://open-ms.sourceforge.net/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>

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>&lt;![CDATA[echo StringTest
+
+&gt; $param_stdout
+]]&gt;</command>
+  <inputs/>
+  <outputs>
+    <data name="param_stdout" format="txt" label="Output from stdout"/>
+  </outputs>
+  <help>&lt;![CDATA[String parameter tests.
+
+
+For more information, visit http://docs.are/unavailable.html]]&gt;</help>
+</tool>