Mercurial > repos > galaxyp > msgfplus
changeset 2:058a2ab1d462 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b4871f9659a924a68430aed3a93f4f9bad733fd6
| author | galaxyp |
|---|---|
| date | Wed, 07 Dec 2016 16:43:17 -0500 |
| parents | 797c755b9e74 |
| children | b4ccaf21855d |
| files | msgfplus.xml test-data/201208-378803-msgf-2mmu-tryptic-many_mods.mzid test-data/201208-378803-msgf-50ppm-semitryptic-no_mods.mzid test-data/201208-378803-msgf_20161026-2mmu-tryptic-many_mods.mzid test-data/201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid |
| diffstat | 5 files changed, 3905 insertions(+), 5675 deletions(-) [+] |
line wrap: on
line diff
--- a/msgfplus.xml Sun Feb 21 11:27:00 2016 -0500 +++ b/msgfplus.xml Wed Dec 07 16:43:17 2016 -0500 @@ -3,7 +3,7 @@ Identifies peptides in tandem mass spectra using the MS-GF+ search engine. </description> <requirements> - <requirement type="package" version="v10089">msgfplus</requirement> + <requirement type="package" version="2016.10.26">msgf_plus</requirement> <environment_variable name="LC_ALL" action="set_to">C</environment_variable> </requirements> <stdio> @@ -12,12 +12,20 @@ <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> </stdio> <command> + <![CDATA[ - #set $db_name = $d.display_name.replace(".fasta", "") + ".fasta" - #set $input_name = $s.display_name + #if $msgf_input.intype_selector == "single" + #set $db_name = $msgf_input.d.display_name.replace(".fasta", "") + ".fasta" + #set $input_name = $msgf_input.s.display_name + ln -s '$msgf_input.s' '${input_name}' && + ln -s '$msgf_input.d' '${db_name}' && + #else if $msgf_input.intype_selector == "fractions" + #set $db_name = $msgf_input.db_spectra.reverse.display_name.replace(".fasta", "") + ".fasta" + #set $input_name = $msgf_input.db_spectra.forward.display_name + ln -s '$msgf_input.db_spectra.forward' '${input_name}' && + ln -s '$msgf_input.db_spectra.reverse' '${db_name}' && + #end if #set $output_name = $input_name.replace(".mzML", "") + ".mzid" - ln -s '$s' '${input_name}' && - ln -s '$d' '${db_name}' && echo \\#Mods > Mods.txt && #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications) @@ -29,10 +37,7 @@ echo '${mod.formula_or_mass},${mod.aa_specificity},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt && #end for - msgfjar=\$(which MSGFPlus.jar) && - ( [ -f "\$msgfjar" ] || (echo MSGFPlus.jar not found && exit 1)) && - - java -jar \$msgfjar + msgf_plus -s '$input_name' -d '$db_name' -thread \${GALAXY_SLOTS:-1} @@ -56,8 +61,20 @@ ]]> </command> <inputs> - <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/> - <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/> + <conditional name="msgf_input"> + <param name="intype_selector" type="select" label="Type of MSGF+ analysis"> + <option value="single">Single database</option> + <option value="fractions">Prefractionated database</option> + </param> + <when value="single"> + <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/> + <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/> + </when> + <when value="fractions"> + <param name="db_spectra" type="data_collection" collection_type="paired" + label="Collection: Pairs of FASTA database (forward) and spectra (reverse)"/> + </when> + </conditional> <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" /> <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/> <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments"> @@ -203,8 +220,21 @@ </outputs> <tests> <test> - <param name="s" value="input/201208-378803.mzML" /> - <param name="d" value="input/cow.protein.PRG2012-subset.fasta" /> + <param name="msgf_input.intype_selector" value="single" /> + <param name="msgf_input.s" value="input/201208-378803.mzML" /> + <param name="msgf_input.d" value="input/cow.protein.PRG2012-subset.fasta" /> + <param name="tda" value="1" /> + <param name="ntt" value="1" /> + <param name="t" value="50" /> + <param name="precursor_ion_tol_units" value="ppm" /> + <param name="common_fixed_modifications" value="" /> + <param name="common_variable_modifications" value="" /> + <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" /> + </test> + <test> + <param name="msgf_input.intype_selector" value="fractions" /> + <param name="msgf_input.db_spectra.forward" value="input/201208-378803.mzML" /> + <param name="msgf_input.db_spectra.reverse" value="input/cow.protein.PRG2012-subset.fasta" /> <param name="tda" value="1" /> <param name="ntt" value="1" /> <param name="t" value="50" /> @@ -214,8 +244,9 @@ <output name="output" file="201208-378803-msgf-50ppm-semitryptic-no_mods.mzid" lines_diff="6" /> </test> <test> - <param name="s" value="input/201208-378803.mzML" /> - <param name="d" value="input/cow.protein.PRG2012-subset.fasta" /> + <param name="msgf_input.intype_selector" value="single" /> + <param name="msgf_input.s" value="input/201208-378803.mzML" /> + <param name="msgf_input.d" value="input/cow.protein.PRG2012-subset.fasta" /> <param name="tda" value="1" /> <param name="t" value="0.02" /> <param name="precursor_ion_tol_units" value="Da" /> @@ -242,12 +273,12 @@ <param name="custom_mods_0|mod_name" value="Gly-loss+Amide" /> <param name="custom_mods_1|formula_or_mass" value="C10H10N5O7P" /> - <param name="custom_mods_1|aa_specificity" value="CS" /> + <param name="custom_mods_1|aa_specificity" value="C,S" /> <param name="custom_mods_1|fix_or_opt" value="opt" /> <param name="custom_mods_1|position_specificity" value="any" /> <param name="custom_mods_1|mod_name" value="cGMP" /> - <output name="output" file="201208-378803-msgf-2mmu-tryptic-many_mods.mzid" lines_diff="6" /> + <output name="output" file="201208-378803-msgf_20161026-2mmu-tryptic-many_mods.mzid" lines_diff="6" /> </test> </tests> <help>
--- a/test-data/201208-378803-msgf-2mmu-tryptic-many_mods.mzid Sun Feb 21 11:27:00 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3039 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<MzIdentML id="MS-GF+" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-11-09T22:47:09" > -<cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> - <cv id="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.30.0" fullName="PSI-MS"/> - <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/> - <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/> -</cvList> -<AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> - <AnalysisSoftware version="Beta (v10089)" name="MS-GF+" id="ID_software"> - <SoftwareName> - <cvParam accession="MS:1002048" cvRef="PSI-MS" name="MS-GF+"/> - </SoftwareName> - </AnalysisSoftware> -</AnalysisSoftwareList> -<SequenceCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> - <DBSequence accession="gi|30794280|ref|NP_851335.1|" searchDatabase_ref="SearchDB_1" length="607" id="DBSeq43937"> - <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|30794280|ref|NP_851335.1| serum albumin precursor [Bos taurus]" name="protein description"/> - </DBSequence> - <DBSequence accession="XXX_gi|528944676|ref|XP_005204734.1|" searchDatabase_ref="SearchDB_1" length="7610" id="DBSeq65480"/> - <DBSequence accession="gi|528968104|ref|XP_005212567.1|" searchDatabase_ref="SearchDB_1" length="815" id="DBSeq27657"> - <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|528968104|ref|XP_005212567.1| PREDICTED: exocyst complex component 6B isoform X1 [Bos taurus]" name="protein description"/> - 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