Mercurial > repos > galaxyp > openms_gnpsexport

diff GNPSExport.xml @ 5:87a970d1514b draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:33:13 +0000
parents 2da14ae3844a
children
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line diff
--- a/GNPSExport.xml	Thu Dec 01 18:57:27 2022 +0000
+++ b/GNPSExport.xml	Fri Jun 14 21:33:13 2024 +0000
@@ -1,9 +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: [File Handling]-->
+<!--Proposed Tool Section: [File Converter]-->
 <tool id="GNPSExport" name="GNPSExport" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format.
-See the documentation on https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms</description>
+  <description>Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format</description>
   <macros>
     <token name="@EXECUTABLE@">GNPSExport</token>
     <import>macros.xml</import>
@@ -16,15 +14,22 @@
 
 ## Preprocessing
 mkdir in_cm &&
-ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
+cp '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
 mkdir in_mzml_cond.in_mzml &&
 #if $in_mzml_cond.in_mzml_select == "no"
 mkdir ${' '.join(["'in_mzml_cond.in_mzml/%s'" % (i) for i, f in enumerate($in_mzml_cond.in_mzml) if f])} && 
-${' '.join(["ln -s '%s' 'in_mzml_cond.in_mzml/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_mzml_cond.in_mzml) if f])}
+${' '.join(["cp '%s' 'in_mzml_cond.in_mzml/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_mzml_cond.in_mzml) if f])}
 #else
-ln -s '$in_mzml_cond.in_mzml' 'in_mzml_cond.in_mzml/${re.sub("[^\w\-_]", "_", $in_mzml_cond.in_mzml.element_identifier)}.$gxy2omsext($in_mzml_cond.in_mzml.ext)' &&
+cp '$in_mzml_cond.in_mzml' 'in_mzml_cond.in_mzml/${re.sub("[^\w\-_]", "_", $in_mzml_cond.in_mzml.element_identifier)}.$gxy2omsext($in_mzml_cond.in_mzml.ext)' &&
 #end if
 mkdir out &&
+mkdir out_quantification &&
+#if "out_pairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_pairs &&
+#end if
+#if "out_meta_values_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_meta_values &&
+#end if
 
 ## Main program call
 
@@ -42,9 +47,29 @@
 #end if
 -out
 'out/output.${gxy2omsext("mgf")}'
+-out_quantification
+'out_quantification/output.${gxy2omsext("txt")}'
+#if "out_pairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_pairs
+  'out_pairs/output.${gxy2omsext("csv")}'
+#end if
+#if "out_meta_values_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_meta_values
+  'out_meta_values/output.${gxy2omsext("tabular")}'
+#end if
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
+#end if
 
 ## Postprocessing
 && mv 'out/output.${gxy2omsext("mgf")}' '$out'
+&& mv 'out_quantification/output.${gxy2omsext("txt")}' '$out_quantification'
+#if "out_pairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_pairs/output.${gxy2omsext("csv")}' '$out_pairs'
+#end if
+#if "out_meta_values_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_meta_values/output.${gxy2omsext("tabular")}' '$out_meta_values'
+#end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -53,47 +78,57 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in_cm" type="data" format="consensusxml" optional="false" label="Input consensusXML file containing only consensusElements with &quot;peptide&quot; annotations" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_cm" type="data" format="consensusxml" label="Input consensusXML file containing only consensusElements with &quot;peptide&quot; annotations" help=" select consensusxml data sets(s)"/>
     <conditional name="in_mzml_cond">
       <param name="in_mzml_select" type="select" label="Run tool in batch mode for -in_mzml">
         <option value="no">No: process all datasets jointly</option>
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in_mzml" type="data" format="mzml" multiple="true" optional="false" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/>
+        <param argument="-in_mzml" type="data" format="mzml" multiple="true" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in_mzml" type="data" format="mzml" multiple="false" optional="false" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/>
+        <param argument="-in_mzml" type="data" format="mzml" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-output_type" type="select" optional="true" label="specificity of mgf output information" help="">
+    <param argument="-output_type" type="select" label="specificity of mgf output information" help="">
       <option value="merged_spectra">merged_spectra</option>
       <option value="most_intense" selected="true">most_intense</option>
       <expand macro="list_string_san" name="output_type"/>
     </param>
-    <param argument="-peptide_cutoff" type="integer" optional="true" min="-1" value="5" label="Number of most intense peptides to consider per consensus element; '-1' to consider all identifications" help=""/>
-    <param argument="-ms2_bin_size" type="float" optional="true" min="0.0" value="0.019999999552965" label="Bin size (Da) for fragment ions when merging ms2 scans" help=""/>
+    <param argument="-peptide_cutoff" type="integer" min="-1" value="5" label="Number of most intense peptides to consider per consensus element; '-1' to consider all identifications" help=""/>
+    <param argument="-ms2_bin_size" type="float" min="0.0" value="0.019999999552965" label="Bin size (Da) for fragment ions when merging ms2 scans" help=""/>
     <section name="merged_spectra" title="Options for exporting mgf file with merged spectra per consensusElement" help="" expanded="false">
-      <param name="cos_similarity" argument="-merged_spectra:cos_similarity" type="float" optional="true" min="0.0" value="0.9" label="Cosine similarity threshold for merged_spectra output" help=""/>
+      <param name="cos_similarity" argument="-merged_spectra:cos_similarity" type="float" min="0.0" value="0.9" label="Cosine similarity threshold for merged_spectra output" help=""/>
     </section>
     <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>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_pairs_FLAG">out_pairs (Output supplementary pairs table for IIMN)</option>
+      <option value="out_meta_values_FLAG">out_meta_values (Output meta value file)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
   <outputs>
     <data name="out" label="${tool.name} on ${on_string}: out" format="mgf"/>
+    <data name="out_quantification" label="${tool.name} on ${on_string}: out_quantification" format="txt"/>
+    <data name="out_pairs" label="${tool.name} on ${on_string}: out_pairs" format="csv">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_pairs_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="out_meta_values" label="${tool.name} on ${on_string}: out_meta_values" format="tabular">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_meta_values_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_GNPSExport_1 -->
-    <test expect_num_outputs="2">
+  <tests>
+    <!-- TOPP_GNPSExport_1 -->
+    <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -102,7 +137,8 @@
       <conditional name="in_mzml_cond">
         <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
       </conditional>
-      <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out" value="GNPSExport_1_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out_quantification" value="GNPSExport_1_out_quant.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="output_type" value="most_intense"/>
       <param name="peptide_cutoff" value="10"/>
       <param name="ms2_bin_size" value="2.0"/>
@@ -115,9 +151,12 @@
           <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>
     <!-- TOPP_GNPSExport_2 -->
-    <test expect_num_outputs="2">
+    <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -126,7 +165,8 @@
       <conditional name="in_mzml_cond">
         <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
       </conditional>
-      <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out" value="GNPSExport_2_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out_quantification" value="GNPSExport_2_out_quant.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="output_type" value="merged_spectra"/>
       <param name="peptide_cutoff" value="10"/>
       <param name="ms2_bin_size" value="2.0"/>
@@ -139,9 +179,12 @@
           <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>
     <!-- TOPP_GNPSExport_3 -->
-    <test expect_num_outputs="2">
+    <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -150,7 +193,8 @@
       <conditional name="in_mzml_cond">
         <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
       </conditional>
-      <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out" value="GNPSExport_3_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out_quantification" value="GNPSExport_3_out_quant.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="output_type" value="most_intense"/>
       <param name="peptide_cutoff" value="10"/>
       <param name="ms2_bin_size" value="0.02"/>
@@ -163,12 +207,45 @@
           <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>
+    <!-- TOPP_GNPSExport_4 -->
+    <test expect_num_outputs="5">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in_cm" value="GNPSExport_cons2.consensusXML"/>
+      <conditional name="in_mzml_cond">
+        <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
+      </conditional>
+      <output name="out" value="GNPSExport_4_out.tmp" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out_quantification" value="GNPSExport_4_out_quant.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out_pairs" value="GNPSExport_4_out_pairs.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out_meta_values" value="GNPSExport_4_out_meta_values.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <param name="output_type" value="most_intense"/>
+      <param name="peptide_cutoff" value="5"/>
+      <param name="ms2_bin_size" value="0.019999999552965"/>
+      <section name="merged_spectra">
+        <param name="cos_similarity" value="0.9"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pairs_FLAG,out_meta_values_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <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[Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format.
 See the documentation on https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_GNPSExport.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_GNPSExport.html]]></help>
   <expand macro="references"/>
 </tool>