Mercurial > repos > galaxyp > percolator

diff test-data/dataset_2.mzid @ 1:86770eea5b09 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
author galaxyp
date Sat, 04 Mar 2017 20:36:03 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataset_2.mzid	Sat Mar 04 20:36:03 2017 -0500
@@ -0,0 +1,381 @@
+<?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="2017-03-01T15:00:34" >
+<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 (v10072)" name="MS-GF+" id="ID_software">
+        <SoftwareName>
+            <cvParam accession="MS:1002048" cvRef="PSI-MS" name="MS-GF+"/>
+        </SoftwareName>
+    </AnalysisSoftware>
+</AnalysisSoftwareList>
+<AnalysisCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
+    <SpectrumIdentification spectrumIdentificationList_ref="SI_LIST_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1">
+        <InputSpectra spectraData_ref="SID_1"/>
+        <SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>
+    </SpectrumIdentification>
+</AnalysisCollection>
+<AnalysisProtocolCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
+    <SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
+        <SearchType>
+            <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/>
+        </SearchType>
+        <AdditionalSearchParams>
+            <cvParam accession="MS:1001211" cvRef="PSI-MS" name="parent mass type mono"/>
+            <cvParam accession="MS:1001256" cvRef="PSI-MS" name="fragment mass type mono"/>
+            <userParam value="false" name="TargetDecoyApproach"/>
+            <userParam value="-1" name="MinIsotopeError"/>
+            <userParam value="2" name="MaxIsotopeError"/>
+            <userParam value="HCD" name="FragmentMethod"/>
+            <userParam value="QExactive" name="Instrument"/>
+            <userParam value="TMT" name="Protocol"/>
+            <userParam value="2" name="NumTolerableTermini"/>
+            <userParam value="1" name="NumMatchesPerSpec"/>
+            <userParam value="2" name="MaxNumModifications"/>
+            <userParam value="6" name="MinPepLength"/>
+            <userParam value="50" name="MaxPepLength"/>
+            <userParam value="2" name="MinCharge"/>
+            <userParam value="6" name="MaxCharge"/>
+        </AdditionalSearchParams>
+        <ModificationParams>
+            <SearchModification residues="M" massDelta="15.994915" fixedMod="false">
+                <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
+            </SearchModification>
+            <SearchModification residues="C" massDelta="57.021465" fixedMod="true">
+                <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/>
+            </SearchModification>
+            <SearchModification residues="K" massDelta="229.16293" fixedMod="true">
+                <cvParam accession="UNIMOD:737" cvRef="UNIMOD" name="TMT6plex"/>
+            </SearchModification>
+            <SearchModification residues="." massDelta="229.16293" fixedMod="true">
+                <SpecificityRules>
+                    <cvParam accession="MS:1001189" cvRef="PSI-MS" name="modification specificity N-term"/>
+                </SpecificityRules>
+                <cvParam accession="UNIMOD:737" cvRef="UNIMOD" name="TMT6plex"/>
+            </SearchModification>
+        </ModificationParams>
+        <Enzymes>
+            <Enzyme missedCleavages="1000" semiSpecific="false" id="Tryp">
+                <EnzymeName>
+                    <cvParam accession="MS:1001251" cvRef="PSI-MS" name="Trypsin"/>
+                </EnzymeName>
+            </Enzyme>
+        </Enzymes>
+        <ParentTolerance>
+            <cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="10.0" name="search tolerance plus value"/>
+            <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="10.0" name="search tolerance minus value"/>
+        </ParentTolerance>
+        <Threshold>
+            <cvParam accession="MS:1001494" cvRef="PSI-MS" name="no threshold"/>
+        </Threshold>
+    </SpectrumIdentificationProtocol>
+</AnalysisProtocolCollection>
+<DataCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
+    <Inputs>
+        <SearchDatabase numDatabaseSequences="102915" location="/mnt/galaxy/data/job_working_directory/000/235/235188/working/dbase.fasta" id="SearchDB_1">
+            <FileFormat>
+                <cvParam accession="MS:1001348" cvRef="PSI-MS" name="FASTA format"/>
+            </FileFormat>
+            <DatabaseName>
+                <userParam name="dbase.fasta"/>
+            </DatabaseName>
+        </SearchDatabase>
+        <SpectraData location="/tmp/tmp_OeEkM/dataset_362460.dat.mzml" name="dataset_362460.dat.mzml" id="SID_1">
+            <FileFormat>
+                <cvParam accession="MS:1000584" cvRef="PSI-MS" name="mzML file"/>
+            </FileFormat>
+            <SpectrumIDFormat>
+                <cvParam accession="MS:1000768" cvRef="PSI-MS" name="Thermo nativeID format"/>
+            </SpectrumIDFormat>
+        </SpectraData>
+    </Inputs>
+    <AnalysisData>
+        <SpectrumIdentificationList id="SI_LIST_1">
+            <FragmentationTable>
+                <Measure id="Measure_MZ">
+                    <cvParam accession="MS:1001225" cvRef="PSI-MS" unitCvRef="PSI-MS" unitName="m/z" unitAccession="MS:1000040" name="product ion m/z"/>
+                </Measure>
+            </FragmentationTable>
+            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=9576" id="SIR_77">
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+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_31443849_362_176"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_31444212_362_184"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_31444767_362_176"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_31445005_362_193"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_31445234_362_184"/>
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+                    <userParam value="-1" name="IsotopeError"/>
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+                    <userParam value="0.008446768" name="ExplainedIonCurrentRatio"/>
+                    <userParam value="0.0048889467" name="NTermIonCurrentRatio"/>
+                    <userParam value="0.003557821" name="CTermIonCurrentRatio"/>
+                    <userParam value="979701.5" name="MS2IonCurrent"/>
+                    <userParam value="4" name="NumMatchedMainIons"/>
+                    <userParam value="7.9951363" name="MeanErrorAll"/>
+                    <userParam value="4.7648582" name="StdevErrorAll"/>
+                    <userParam value="7.9951363" name="MeanErrorTop7"/>
+                    <userParam value="4.7648582" name="StdevErrorTop7"/>
+                    <userParam value="0.79569435" name="MeanRelErrorAll"/>
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+                    <userParam value="0.79569435" name="MeanRelErrorTop7"/>
+                    <userParam value="9.273238" name="StdevRelErrorTop7"/>
+                </SpectrumIdentificationItem>
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+            </SpectrumIdentificationResult>
+            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=9739" id="SIR_240">
+                <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep363" calculatedMassToCharge="1044.435546875" experimentalMassToCharge="1045.4466552734375" chargeState="2" id="SII_240_1">
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_36274231_363_1"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_36275421_363_1"/>
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+                    <cvParam accession="MS:1002053" cvRef="PSI-MS" value="49910.527" name="MS-GF:EValue"/>
+                    <userParam value="2" name="IsotopeError"/>
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+                    <userParam value="0.04388853" name="ExplainedIonCurrentRatio"/>
+                    <userParam value="0.0018504228" name="NTermIonCurrentRatio"/>
+                    <userParam value="0.04203811" name="CTermIonCurrentRatio"/>
+                    <userParam value="211725.44" name="MS2IonCurrent"/>
+                    <userParam value="3" name="NumMatchedMainIons"/>
+                    <userParam value="5.0645747" name="MeanErrorAll"/>
+                    <userParam value="4.3375416" name="StdevErrorAll"/>
+                    <userParam value="5.0645747" name="MeanErrorTop7"/>
+                    <userParam value="4.3375416" name="StdevErrorTop7"/>
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+                    <userParam value="4.3375416" name="StdevRelErrorAll"/>
+                    <userParam value="-5.0645747" name="MeanRelErrorTop7"/>
+                    <userParam value="4.3375416" name="StdevRelErrorTop7"/>
+                </SpectrumIdentificationItem>
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+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_2219651_364_124"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_2220892_364_124"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_2221016_364_118"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_2222191_364_118"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_2223367_364_124"/>
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+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_2224990_364_94"/>
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+                </SpectrumIdentificationItem>
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+            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=9594" id="SIR_95">
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+                    <userParam value="1176358.8" name="MS2IonCurrent"/>
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+            </SpectrumIdentificationResult>
+            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=9681" id="SIR_182">
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+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_8122856_371_29"/>
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_8123174_371_89"/>
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+            </SpectrumIdentificationResult>
+        </SpectrumIdentificationList>
+    </AnalysisData>
+</DataCollection>
+</MzIdentML>