diff SpecLibSearcher.xml @ 8:3aa3b656e624 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

--- a/SpecLibSearcher.xml	Fri Nov 06 20:40:25 2020 +0000
+++ b/SpecLibSearcher.xml	Thu Dec 01 19:12:08 2022 +0000
@@ -1,13 +1,11 @@
 <?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: [Identification]-->
-<tool id="SpecLibSearcher" name="SpecLibSearcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="SpecLibSearcher" name="SpecLibSearcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.</description>
   <macros>
     <token name="@EXECUTABLE@">SpecLibSearcher</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -16,11 +14,17 @@
 #import re
 
 ## Preprocessing
-mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir in_cond.in &&
+#if $in_cond.in_select == "no"
+mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
+${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+#end if
 mkdir lib &&
 ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
 mkdir out &&
+mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
 
 ## Main program call
 
@@ -29,14 +33,18 @@
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+#if $in_cond.in_select == "no"
+${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
+#end if
 -lib
 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)'
 -out
-${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("idxml")) for _ in $in if _])}
+${' '.join(["'out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("idxml")) for i, f in enumerate($in_cond.in) if f])}
 
 ## Postprocessing
-${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("idxml")} for _ in $out if _])}
+${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("idxml")} for i, f in enumerate($in_cond.in) if f])}
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -45,28 +53,39 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files" help=" select mzml data sets(s)"/>
-    <param name="lib" argument="-lib" type="data" format="msp" optional="false" label="searchable spectral library (MSP format)" help=" select msp data sets(s)"/>
-    <param name="compare_function" argument="-compare_function" type="select" optional="false" label="function for similarity comparison" help="">
+    <conditional name="in_cond">
+      <param name="in_select" type="select" label="Run tool in batch mode for -in">
+        <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" type="data" format="mzml" multiple="true" optional="false" label="Input files" help=" select mzml data sets(s)"/>
+      </when>
+      <when value="yes">
+        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files" help=" select mzml data sets(s)"/>
+      </when>
+    </conditional>
+    <param argument="-lib" type="data" format="msp" optional="false" label="searchable spectral library (MSP format)" help=" select msp data sets(s)"/>
+    <param argument="-compare_function" type="select" optional="true" label="function for similarity comparison" help="">
       <option value="PeakAlignment">PeakAlignment</option>
       <option value="SpectrumAlignmentScore">SpectrumAlignmentScore</option>
       <option value="SpectrumCheapDPCorr">SpectrumCheapDPCorr</option>
       <option value="SpectrumPrecursorComparator">SpectrumPrecursorComparator</option>
       <option value="SteinScottImproveScore">SteinScottImproveScore</option>
       <option value="ZhangSimilarityScore" selected="true">ZhangSimilarityScore</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="compare_function"/>
     </param>
     <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
       <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/>
-      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
+      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="mass_tolerance_unit"/>
       </param>
       <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/>
       <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/>
       <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-        <expand macro="list_integer_valsan"/>
+        <expand macro="list_integer_valsan" name="isotopes"/>
       </param>
     </section>
     <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false">
@@ -83,7 +102,6 @@
     </section>
     <section name="modifications" title="Modifications Options" help="" expanded="false">
       <param name="fixed" argument="-modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
-        <option value="">default (nothing chosen)</option>
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -1453,7 +1471,6 @@
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
@@ -3012,10 +3029,9 @@
         <option value="ZGB (K)">ZGB (K)</option>
         <option value="ZGB (N-term)">ZGB (N-term)</option>
         <option value="ZQG (K)">ZQG (K)</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="fixed"/>
       </param>
       <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
-        <option value="">default (nothing chosen)</option>
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -4385,7 +4401,6 @@
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
@@ -5944,14 +5959,14 @@
         <option value="ZGB (K)">ZGB (K)</option>
         <option value="ZGB (N-term)">ZGB (N-term)</option>
         <option value="ZQG (K)">ZQG (K)</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="variable"/>
       </param>
       <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san"/>
+      <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="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -5960,19 +5975,59 @@
   </inputs>
   <outputs>
     <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
-      <discover_datasets directory="out" format="idxml" pattern="__name__"/>
+      <discover_datasets directory="out" recurse="true" format="idxml" pattern="__name__"/>
     </collection>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_SpecLibSearcher"/>
-    <expand macro="manutest_SpecLibSearcher"/>
+  <tests><!-- TOPP_SpecLibSearcher_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="SpecLibSearcher_1.mzML"/>
+      </conditional>
+      <param name="lib" value="SpecLibSearcher_1.MSP"/>
+      <output_collection name="out" count="1"/>
+      <param name="compare_function" value="ZhangSimilarityScore"/>
+      <section name="precursor">
+        <param name="mass_tolerance" value="3.0"/>
+        <param name="mass_tolerance_unit" value="Da"/>
+        <param name="min_charge" value="1"/>
+        <param name="max_charge" value="5"/>
+        <param name="isotopes" value="0 1"/>
+      </section>
+      <section name="fragment">
+        <param name="mass_tolerance" value="10.0"/>
+      </section>
+      <section name="report">
+        <param name="top_hits" value="10"/>
+      </section>
+      <section name="filter">
+        <param name="remove_peaks_below_threshold" value="2.01"/>
+        <param name="min_peaks" value="5"/>
+        <param name="max_peaks" value="150"/>
+        <param name="cut_peaks_below" value="1000"/>
+      </section>
+      <section name="modifications">
+        <param name="fixed"/>
+        <param name="variable"/>
+        <param name="variable_max_per_peptide" value="2"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SpecLibSearcher.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpecLibSearcher.html]]></help>
   <expand macro="references"/>
 </tool>