# HG changeset patch
# User galaxyp
# Date 1666713980 0
# Node ID 3b2874c58bcd71404e53b91e0707a51ca525cb97
# Parent  6b5ce9e2b0d012749f0e762d30bd6fe606a12cd8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071

diff -r 6b5ce9e2b0d0 -r 3b2874c58bcd pepquery2.xml
--- a/pepquery2.xml	Sun Oct 02 23:50:18 2022 +0000
+++ b/pepquery2.xml	Tue Oct 25 16:06:20 2022 +0000
@@ -32,6 +32,7 @@
 #end if
 ## PepQuery command
 pepquery 
+  -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g
 #if $validation.task_type == "known"
   -s 2 $validation.decoy
 #else
@@ -49,26 +50,33 @@
   -db '$req_inputs.db_type.db_id' 
 #end if
 #if $req_inputs.input_type.input_type_selector == 'peptide'
-  -t '$req_inputs.input_type.input_type_selector'
+  -t $req_inputs.input_type.input_type_selector
   -i '$req_inputs.input_type.multiple.input'
 #else
-  -t '$req_inputs.input_type.input_type_selector'
-  #if int(str($req_inputs.input_type.input_type_selector)) == 1
-    -i '$req_inputs.input_type.multiple.input'
+  -t $req_inputs.input_type.input_type_selector
+  #if $req_inputs.input_type.input_type_selector == 'protein'
+    #if $req_inputs.input_type.multiple.protein_input_selector == 'identifier'
+      #set $prot_id = str($req_inputs.input_type.multiple.input).replace('|','\|')
+      -i '"$prot_id"'
+    #else
+      -i '$req_inputs.input_type.multiple.input'
+    #end if
   #else
     -i '$req_inputs.input_type.input'
-    #if int(str($req_inputs.input_type.input_type_selector)) == 2
+    #if $req_inputs.input_type.input_type_selector == 'DNA'
       #if $req_inputs.input_type.frame == 'None'
-        -f '0'
+        -frame '0'
       #else
-        -f '$req_inputs.input_type.frame'
+        -frame '$req_inputs.input_type.frame'
       #end if
     #else
             -anno '$req_inputs.input_type.anno'
     #end if
   #end if
 #end if
+#if $req_inputs.indexType
   -indexType $req_inputs.indexType
+#end if
 
 #if $modifications.fixed_mod
   -fixMod '$modifications.fixed_mod'
@@ -134,8 +142,8 @@
 #end if
   $fast
   -o pepquery_output
-  | sed 's/No valid peptide/Error: No valid peptide/' | tee >(cat 1>&2)
-#set $flist = str($outputs_selected).replace(',',' ') 
+  | tee >(sed "s/\x1b[^m]*m//g" > log.txt) 
+#set $flist = str($outputs_selected).replace(',',' ').replace('ms_index','')
 && for i in $flist; do for f in `find pepquery_output/*/* -name \$i`; do cat \$f >> pepquery_output/\${i}; done; done
 && for f in `find pepquery_output/*/ -name parameter.txt`; do cp \$f pepquery_output/parameter.txt; done 
         ]]>
@@ -155,8 +163,8 @@
             <conditional name="input_type">
                 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
                     <option value="peptide">peptide</option>
-                    <option value="1">protein</option>
-                    <option value="2">DNA (translate to protein sequences)</option>
+                    <option value="protein">protein</option>
+                    <option value="DNA">DNA (translate to protein sequences)</option>
                     <!-- these are not working with pepquery version 1.6
                     <option value="3">VCF (translate to protein sequences)</option>
                     <option value="4">BED (translate to protein sequences)</option>
@@ -170,7 +178,11 @@
                             <option value="single">Single peptide entered as text</option>
                         </param> 
                         <when value="multiple">
-                            <param name="input" argument="-i" type="data" format="txt" label="Peptide Sequences (.txt)" help="Peptide sequence file containing peptides which you want to search (no column header, 1 peptide per line)." />
+                            <param name="input" argument="-i" type="data" format="txt" label="Peptide Sequences (.txt)">
+                                <help>Peptide sequence file containing peptides which you want to search (no column headers).
+                                      First column is am peptide sequence. Optional second column is spectrum title.
+                                </help>
+                            </param>
                         </when>
                         <when value="single">
                             <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search">
@@ -179,11 +191,12 @@
                         </when>
                     </conditional>
                 </when>
-                <when value="1">
+                <when value="protein">
                     <conditional name="multiple">
                         <param name="protein_input_selector" type="select" label="Proteins?">
                             <option value="multiple">Protein fasta from your history</option>
                             <option value="single">Single protein entered as text</option>
+                            <option value="identifier">Protein Identifier from selected Protein Reference Database</option>
                         </param> 
                         <when value="multiple">
                             <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." />
@@ -193,9 +206,19 @@
                                 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
                             </param>
                         </when>
+                        <when value="identifier">
+                            <param name="input" argument="-i" type="text" label="Protein Identifier" help="Protein ID from the selected Protein Reference Database. E.g. sp|P07205|PGK2_HUMAN from swissprot:human">
+                                <sanitizer invalid_char="">
+                                    <valid initial="string.ascii_letters,string.digits">
+                                        <add value="|" />
+                                    </valid>
+                                </sanitizer>
+                                <validator type="regex" message="Spaces not allowed in ID">^[^ ]+$</validator>
+                            </param>
+                        </when>
                     </conditional>
                 </when>
-                <when value="2">
+                <when value="DNA">
                     <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search">
                         <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator>
                     </param> 
@@ -268,8 +291,8 @@
                 </when>
             </conditional>
 
-            <param name="indexType" argument="-indexType" type="select" label="Report Spectrum Scan as" help="" >
-                <option value="1" selected="true">index (1-based) in MGF</option>
+            <param name="indexType" argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
+                <option value="1">index (1-based) in MGF</option>
                 <option value="2">spectrum title in MGF</option>
             </param>
         </section>
@@ -289,11 +312,11 @@
 
         <section name="modifications" title="Modifications" expanded="false">
              <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" optional="true">
-                <help>default: 1: Carbamidomethylation of C [57.02146372057]</help>
+                <help>Default: 1: Carbamidomethylation of C [57.02146372057]</help>
                 <expand macro="modifications" />
              </param>
              <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" optional="true">
-                <help>default: 2: Oxidation of M [15.99491461956]</help>
+                <help>Default: 2: Oxidation of M [15.99491461956]</help>
                 <expand macro="modifications" />
              </param>
 
@@ -303,9 +326,9 @@
         </section>
 
         <section name="digestion" title="Digestion" expanded="false">
-            <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion" >
+            <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion.  Default: Trypsin" >
                 <option value="0">Non enzyme</option>
-                <option value="1" selected="true">Trypsin</option>
+                <option value="1">Trypsin</option>
                 <option value="2">Trypsin (no P rule)</option>
                 <option value="3">Arg-C</option>
                 <option value="4">Arg-C (no P rule)</option>
@@ -319,20 +342,20 @@
         <section name="ms_params" title="Mass spectrometer" expanded="false">
             <section name="tolerance_params" title="Tolerance" expanded="true">
                 <param name="precursor_tolerance" argument="-tol" type="integer" value="" optional="true" label="Precursor Tolerance" help="The error window on experimental peptide mass values. This parameter is usually set according to the mass spectrometer which was used to generate the MS/MS data.  Default: 10" />
-                <param name="precursor_unit" argument="-tolu" type="select" optional="true" label="Precursor Unit" help="The unit of precursor ion m/z tolerance">
-                    <option value="ppm" selected="true">ppm</option>
+                <param name="precursor_unit" argument="-tolu" type="select" optional="true" label="Precursor Unit" help="The unit of precursor ion m/z tolerance. Default: ppm">
+                    <option value="ppm">ppm</option>
                     <option value="Da">Da</option>
                 </param>
                 <param name="tolerance" argument="-itol" type="float" value="" optional="true" label="Tolerance" help="Error window for MS/MS fragment ion mass values in Da unit.  Default: 0.6 Da" />
             </section>
 
             <section name="search" title="PSM" expanded="false">
-                <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method">
-                    <option value="1" selected="true">CID/HCD</option>
+                <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method" help="Default: CID/HCD">
+                    <option value="1">CID/HCD</option>
                     <option value="2">ETD</option>
                 </param>
-                <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method">
-                    <option value="1" selected="true">HyperScore</option>
+                <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method" help="Default: HyperScore">
+                    <option value="1">HyperScore</option>
                     <option value="2">MVH</option>
                 </param>
                 <param name="extra_score_validation" argument="-x" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Add extra score validation" help="use two scoring algorithms for peptide identification" />
@@ -359,12 +382,13 @@
             <option value="detail.txt" selected="true">detail.txt</option>
             <option value="ptm.txt" selected="true">ptm.txt</option>
             <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option>
-            <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option>
             <option value="ms_index" selected="true">MS/MS Index</option>
         </param>
         <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
     </inputs>
     <outputs>
+        <data name="log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
+        </data> 
         <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">
         </data> 
         <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt">
diff -r 6b5ce9e2b0d0 -r 3b2874c58bcd test-data/AgilentMassHunterTest.mzXML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/AgilentMassHunterTest.mzXML	Tue Oct 25 16:06:20 2022 +0000
@@ -0,0 +1,4263 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">
+  <msRun scanCount="212" startTime="PT0.668S" endTime="PT209.708S">
+    <msInstrument msInstrumentID="1">
+      <msManufacturer category="msManufacturer" value="instrument model"/>
+      <msModel category="msModel" value="Agilent instrument model"/>
+      <msIonisation category="msIonisation" value="microelectrospray"/>
+      <msMassAnalyzer category="msMassAnalyzer" value="time-of-flight"/>
+      <msDetector category="msDetector" value="microchannel plate detector"/>
+      <software type="acquisition" name="MassHunter Data Acquisition" version="8.0"/>
+    </msInstrument>
+    <dataProcessing>
+      <software type="conversion" name="ProteoWizard software" version="3.0.20287"/>
+      <processingOperation name="Conversion to mzML"/>
+    </dataProcessing>
+    <scan num="676"
+          scanType="Full"
+          centroided="1"
+          msLevel="1"
+          peaksCount="164"
+          polarity="+"
+          retentionTime="PT0.668S"
+          lowMz="101.059547842973"
+          highMz="961.958412367698"
+          basePeakMz="622.030137146612"
+          basePeakIntensity="69123.5234"
+          totIonCurrent="248205.188"
+          msInstrumentID="1">
+      <peaks compressionType="zlib"
+             compressedLen="2042"
+             precision="64"
+             byteOrder="network"
+             contentType="m/z-int">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</peaks>
+    </scan>
+    <scan num="1667"
+          scanType="Full"
+          centroided="1"
+          msLevel="1"
+          peaksCount="154"
+          polarity="+"
+          retentionTime="PT1.659S"
+          lowMz="101.058882937497"
+          highMz="960.969890733779"
+          basePeakMz="622.030314834219"
+          basePeakIntensity="66012.125"
+          totIonCurrent="242169.563"
+          msInstrumentID="1">
+      <peaks compressionType="zlib"
+             compressedLen="1910"
+             precision="64"
+             byteOrder="network"
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diff -r 6b5ce9e2b0d0 -r 3b2874c58bcd test-data/small-index-filter.mzML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small-index-filter.mzML	Tue Oct 25 16:06:20 2022 +0000
@@ -0,0 +1,514 @@
+<?xml version="1.0" encoding="utf-8"?>
+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
+  <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="small" version="1.1.0">
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+      <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>
+    </cvList>
+    <fileDescription>
+      <fileContent>
+        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
+        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
+      </fileContent>
+      <sourceFileList count="3">
+        <sourceFile id="RAW1" name="small.RAW" location="file:///">
+          <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>
+        </sourceFile>
+        <sourceFile id="small.mzML" name="small.mzML" location="file:///">
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>
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+        <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">
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+      </software>
+    </softwareList>
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+          </analyzer>
+          <detector order="3">
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+          </detector>
+        </componentList>
+        <softwareRef ref="Xcalibur"/>
+      </instrumentConfiguration>
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+        <referenceableParamGroupRef ref="CommonInstrumentParams"/>
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+          <source order="1">
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+          </detector>
+        </componentList>
+        <softwareRef ref="Xcalibur"/>
+      </instrumentConfiguration>
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+          <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
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+      </dataProcessing>
+    </dataProcessingList>
+    <run id="small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2005-07-20T14:44:22Z" defaultSourceFileRef="RAW1">
+      <spectrumList count="7" defaultDataProcessingRef="pwiz_Reader_conversion">
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