diff MetaboliteSpectralMatcher.xml @ 14:e46a9e72c395 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

--- a/MetaboliteSpectralMatcher.xml	Thu Dec 01 19:02:30 2022 +0000
+++ b/MetaboliteSpectralMatcher.xml	Fri Jun 14 21:31:08 2024 +0000
@@ -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: [Metabolite Identification]-->
 <tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Perform a spectral library search.</description>
+  <description>Perform a spectral library search</description>
   <macros>
     <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
     <import>macros.xml</import>
@@ -15,10 +14,13 @@
 
 ## 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($in.ext)' &&
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 mkdir out &&
+#if "out_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_spectra &&
+#end if
 
 ## Main program call
 
@@ -32,9 +34,19 @@
 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
 -out
 'out/output.${gxy2omsext("mztab")}'
+#if "out_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_spectra
+  'out_spectra/output.${gxy2omsext("mzml")}'
+#end if
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
+#end if
 
 ## Postprocessing
 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
+#if "out_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_spectra/output.${gxy2omsext("mzml")}' '$out_spectra'
+#end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -43,54 +55,61 @@
     <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 spectra" help=" select mzml data sets(s)"/>
-    <param argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input spectra" help=" select mzml data sets(s)"/>
+    <param argument="-database" type="data" format="mgf,msp,mzml" label="Default spectral database" help=" select mgf,msp,mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="prec_mass_error_value" argument="-algorithm:prec_mass_error_value" type="float" optional="true" value="100.0" label="Error allowed for precursor ion mass" help=""/>
-      <param name="frag_mass_error_value" argument="-algorithm:frag_mass_error_value" type="float" optional="true" value="500.0" label="Error allowed for product ions" help=""/>
-      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="true" label="Unit of mass error (ppm or Da)" help="">
+      <param name="prec_mass_error_value" argument="-algorithm:prec_mass_error_value" type="float" value="100.0" label="Error allowed for precursor ion mass" help=""/>
+      <param name="frag_mass_error_value" argument="-algorithm:frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions" help=""/>
+      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" label="Unit of mass error (ppm or Da)" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_error_unit"/>
       </param>
-      <param name="report_mode" argument="-algorithm:report_mode" type="select" optional="true" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
+      <param name="report_mode" argument="-algorithm:report_mode" type="select" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
         <option value="top3" selected="true">top3</option>
         <option value="best">best</option>
         <expand macro="list_string_san" name="report_mode"/>
       </param>
-      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="true" label="Positive or negative ionization mode?" help="">
+      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" label="Positive or negative ionization mode?" help="">
         <option value="positive" selected="true">positive</option>
         <option value="negative">negative</option>
         <expand macro="list_string_san" name="ionization_mode"/>
       </param>
+      <param name="merge_spectra" argument="-algorithm:merge_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Merge MS2 spectra with the same precursor mass" 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_spectra_FLAG">out_spectra (Output spectra as mzML file)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
   <outputs>
     <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
+    <data name="out_spectra" label="${tool.name} on ${on_string}: out_spectra" format="mzml">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_spectra_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="spectra.mzML"/>
-    <param name="database" value="MetaboliteSpectralDB.mzML"/>
-    <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/>
-  </test>
-</tests>
+  <tests>
+    <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
+    <test expect_num_outputs="1">
+      <!-- same input as used in the MSGF+Adapter, used as input and database -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="spectra.mzML"/>
+      <param name="database" value="MetaboliteSpectralDB.mzML"/>
+      <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/>
+    </test>
+  </tests>
   <help><![CDATA[Perform a spectral library search.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaboliteSpectralMatcher.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MetaboliteSpectralMatcher.html]]></help>
   <expand macro="references"/>
 </tool>