Merge pull request #697 from bernt-matthias/openms2.9

OpenMS 3.1
galaxyproteomics · Jun 14, 2024 · 5c080b1 · 5c080b1
2 parents fd12c12 + fd81607
commit 5c080b1
Show file tree

Hide file tree

Showing 182 changed files with 9,776 additions and 36,115 deletions.
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -285,6 +285,17 @@ jobs:
       with:
         path: ~/.planemo
         key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+#     # TODO this is only temporary and only for OpenMS
+    - name: create test data
+      run: |
+           echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt
+           while read repo
+           do
+               if [ -x $repo/test-data.sh ]; then
+                   cd $repo
+                   ./test-data.sh
+               fi
+           done < repository_list.txt
     - name: Get number of CPU cores
       uses: SimenB/github-actions-cpu-cores@v2
       id: cpu-cores

diff --git a/tools/openms/.shed.yml b/tools/openms/.shed.yml
@@ -12,7 +12,6 @@ categories:
 - Proteomics
 exclude:
 - aux/
-- generate.sh
 auto_tool_repositories:
   name_template: "openms_{{ tool_id }}"
   description_template: "Wrapper for the OpenMS suite tool: {{ tool_name }}"

diff --git a/tools/openms/AccurateMassSearch.xml b/tools/openms/AccurateMassSearch.xml
diff --git a/tools/openms/AssayGeneratorMetabo.xml b/tools/openms/AssayGeneratorMetabo.xml
diff --git a/tools/openms/BaselineFilter.xml b/tools/openms/BaselineFilter.xml
@@ -1,8 +1,7 @@
-<?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: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Removes the baseline from profile spectra using a top-hat filter.</description>
+  <description>Removes the baseline from profile spectra using a top-hat filter</description>
   <macros>
     <token name="@EXECUTABLE@">BaselineFilter</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,14 +38,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
-    <param argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
-    <param argument="-struc_elem_unit" type="select" optional="true" label="Unit of 'struc_elem_length' paramete" help="">
+    <param argument="-in" type="data" format="mzml" label="input raw data file" help=" select mzml data sets(s)"/>
+    <param argument="-struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
+    <param argument="-struc_elem_unit" type="select" label="Unit of 'struc_elem_length' paramete" help="">
       <option value="Thomson" selected="true">Thomson</option>
       <option value="DataPoints">DataPoints</option>
       <expand macro="list_string_san" name="struc_elem_unit"/>
     </param>
-    <param argument="-method" type="select" optional="true" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
+    <param argument="-method" type="select" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
       <option value="identity">identity</option>
       <option value="erosion">erosion</option>
       <option value="dilation">dilation</option>
@@ -61,7 +60,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -75,14 +74,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_BaselineFilter_1 -->
+  <tests>
+    <!-- TOPP_BaselineFilter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="BaselineFilter_input.mzML"/>
-      <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="struc_elem_length" value="1.5"/>
       <param name="struc_elem_unit" value="Thomson"/>
       <param name="method" value="tophat"/>
@@ -92,11 +92,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_BaselineFilter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_BaselineFilter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/CVInspector.xml b/tools/openms/CVInspector.xml
@@ -1,8 +1,7 @@
-<?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]-->
+<!--Proposed Tool Section: [[for Developers]]-->
 <tool id="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>A tool for visualization and validation of PSI mapping and CV files.</description>
+  <description>A tool for visualization and validation of PSI mapping and CV files</description>
   <macros>
     <token name="@EXECUTABLE@">CVInspector</token>
     <import>macros.xml</import>
@@ -17,12 +16,12 @@
 mkdir cv_files_cond.cv_files &&
 #if $cv_files_cond.cv_files_select == "no"
 mkdir ${' '.join(["'cv_files_cond.cv_files/%s'" % (i) for i, f in enumerate($cv_files_cond.cv_files) if f])} && 
-${' '.join(["ln -s '%s' 'cv_files_cond.cv_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])}
+${' '.join(["cp '%s' 'cv_files_cond.cv_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])}
 #else
-ln -s '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' &&
+cp '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' &&
 #end if
 mkdir mapping_file &&
-ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
+cp '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir html &&
 #end if
@@ -67,24 +66,24 @@ ${' '.join(["'cv_files_cond.cv_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.el
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-cv_files" type="data" format="obo" multiple="true" optional="false" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
+        <param argument="-cv_files" type="data" format="obo" multiple="true" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-cv_files" type="data" format="obo" multiple="false" optional="false" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
+        <param argument="-cv_files" type="data" format="obo" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-cv_names" type="text" optional="false" value="" label="List of identifiers (one for each ontology file)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-cv_names" type="text" value="" label="List of identifiers (one for each ontology file)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="cv_names"/>
       <expand macro="list_string_san" name="cv_names"/>
     </param>
-    <param argument="-mapping_file" type="data" format="xml" optional="false" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/>
-    <param argument="-ignore_cv" type="text" optional="true" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-mapping_file" type="data" format="xml" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/>
+    <param argument="-ignore_cv" type="text" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="ignore_cv"/>
       <expand macro="list_string_san" name="ignore_cv"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -104,19 +103,20 @@ ${' '.join(["'cv_files_cond.cv_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.el
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml -->
-  <test expect_num_outputs="1">
-    <param name="adv_opts|test" value="true"/>
-    <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>
-    <param name="cv_names" value="XLMOD"/>
-    <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>
-    <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>
-    <output name="html" ftype="html" value="CVInspector.html"/>
-  </test>
-</tests>
+  <tests>
+    <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml -->
+    <test expect_num_outputs="1">
+      <param name="adv_opts|test" value="true"/>
+      <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>
+      <param name="cv_names" value="XLMOD"/>
+      <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>
+      <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>
+      <output name="html" ftype="html" value="CVInspector.html"/>
+    </test>
+  </tests>
   <help><![CDATA[A tool for visualization and validation of PSI mapping and CV files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_CVInspector.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_CVInspector.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/ClusterMassTraces.xml b/tools/openms/ClusterMassTraces.xml
@@ -1,8 +1,7 @@
-<?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]-->
+<!--Proposed Tool Section: [Misc / Helpers]-->
 <tool id="ClusterMassTraces" name="ClusterMassTraces" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Creates pseudo spectra.</description>
+  <description>Creates pseudo spectra</description>
   <macros>
     <token name="@EXECUTABLE@">ClusterMassTraces</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,16 +38,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml" optional="false" label="Mass traces" help=" select consensusxml data sets(s)"/>
-    <param argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score" help=""/>
-    <param argument="-min_peak_nr" type="integer" optional="true" value="1" label="Minimal peak nr to output pseudo spectra" help=""/>
-    <param argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help=""/>
-    <param argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time" help=""/>
-    <param argument="-max_intensity_cutoff" type="float" optional="true" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/>
-    <param argument="-add_precursor" type="float" optional="true" value="0.0" label="Add a precursor mass" help=""/>
+    <param argument="-in" type="data" format="consensusxml" label="Mass traces" help=" select consensusxml data sets(s)"/>
+    <param argument="-min_pearson_correlation" type="float" value="0.7" label="Minimal pearson correlation score" help=""/>
+    <param argument="-min_peak_nr" type="integer" value="1" label="Minimal peak nr to output pseudo spectra" help=""/>
+    <param argument="-max_lag" type="integer" value="1" label="Maximal lag" help=""/>
+    <param argument="-max_rt_apex_difference" type="float" value="5.0" label="Maximal difference of the apex in retention time" help=""/>
+    <param argument="-max_intensity_cutoff" type="float" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/>
+    <param argument="-add_precursor" type="float" value="0.0" label="Add a precursor mass" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -62,15 +61,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- test with arbitarily chosen consensusXML -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
+      <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/>
+    </test>
+  </tests>
   <help><![CDATA[Creates pseudo spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ClusterMassTraces.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ClusterMassTraces.html]]></help>
   <expand macro="references"/>
 </tool>