Mercurial > repos > galaxyp > bibliospec
annotate test-data/msgf-test.mzid @ 0:5a4801b7d106 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
| author | galaxyp |
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| date | Tue, 08 May 2018 14:16:45 -0400 |
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| rev | line source |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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1 <?xml version="1.0" encoding="UTF-8"?> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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2 <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="2014-01-17T14:17:27" > |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
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3 <cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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4 <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"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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5 <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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6 <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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7 </cvList> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
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8 <AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
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9 <AnalysisSoftware version="Beta (v9881)" name="MS-GF+" id="ID_software"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
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10 <SoftwareName> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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11 <cvParam accession="MS:1002048" cvRef="PSI-MS" name="MS-GF+"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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12 </SoftwareName> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
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13 </AnalysisSoftware> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
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14 </AnalysisSoftwareList> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
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15 <SequenceCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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16 <DBSequence accession="gi|24373345|ref|NP_717388.1|" searchDatabase_ref="SearchDB_1" length="735" id="DBSeq1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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17 <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24373345|ref|NP_717388.1| extracelllular iron oxide respiratory system surface decaheme cytochrome c component OmcA [Shewanella oneidensis MR-1]" name="protein description"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
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18 </DBSequence> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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19 <DBSequence accession="gi|24371739|ref|NP_715781.1|" searchDatabase_ref="SearchDB_1" length="178" id="DBSeq737"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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20 <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24371739|ref|NP_715781.1| ferritin Ftn [Shewanella oneidensis MR-1]" name="protein description"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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21 </DBSequence> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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22 <DBSequence accession="gi|24371954|ref|NP_715996.1|" searchDatabase_ref="SearchDB_1" length="400" id="DBSeq1994"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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23 <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24371954|ref|NP_715996.1| ISSod4 transposase TnpA_ISSod4 [Shewanella oneidensis MR-1]" name="protein description"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
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24 </DBSequence> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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25 <DBSequence accession="gi|24373023|ref|NP_717065.1|" searchDatabase_ref="SearchDB_1" length="188" id="DBSeq1805"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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26 <cvParam accession="MS:1001088" cvRef="PSI-MS" value="gi|24373023|ref|NP_717065.1| site-specific recombinase phage integrase family [Shewanella oneidensis MR-1]" name="protein description"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
parents:
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27 </DBSequence> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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28 <Peptide id="Pep1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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29 <PeptideSequence>FKWNGTDTNSAAEK</PeptideSequence> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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30 </Peptide> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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31 <Peptide id="Pep2"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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32 <PeptideSequence>GGESIMNAQSQPQA</PeptideSequence> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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33 </Peptide> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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34 <Peptide id="Pep3"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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35 <PeptideSequence>VIYTTNAVEAVHRQFRKLTK</PeptideSequence> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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36 </Peptide> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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37 <Peptide id="Pep4"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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38 <PeptideSequence>VMRMLR</PeptideSequence> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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39 </Peptide> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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40 <PeptideEvidence isDecoy="false" post="R" pre="R" end="556" start="543" peptide_ref="Pep1" dBSequence_ref="DBSeq1" id="PepEv_543_1_543"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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41 <PeptideEvidence isDecoy="false" post="-" pre="K" end="178" start="165" peptide_ref="Pep2" dBSequence_ref="DBSeq737" id="PepEv_901_2_165"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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42 <PeptideEvidence isDecoy="false" post="T" pre="K" end="346" start="327" peptide_ref="Pep3" dBSequence_ref="DBSeq1994" id="PepEv_2320_3_327"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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43 <PeptideEvidence isDecoy="false" post="H" pre="R" end="161" start="156" peptide_ref="Pep4" dBSequence_ref="DBSeq1805" id="PepEv_1960_4_156"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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44 </SequenceCollection> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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45 <AnalysisCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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46 <SpectrumIdentification spectrumIdentificationList_ref="SI_LIST_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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47 <InputSpectra spectraData_ref="SID_1"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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48 <SearchDatabaseRef searchDatabase_ref="SearchDB_1"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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49 </SpectrumIdentification> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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50 </AnalysisCollection> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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51 <AnalysisProtocolCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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52 <SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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53 <SearchType> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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54 <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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55 </SearchType> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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56 <AdditionalSearchParams> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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57 <cvParam accession="MS:1001211" cvRef="PSI-MS" name="parent mass type mono"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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58 <cvParam accession="MS:1001256" cvRef="PSI-MS" name="fragment mass type mono"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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59 <userParam value="true" name="TargetDecoyApproach"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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60 <userParam value="-1" name="MinIsotopeError"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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61 <userParam value="2" name="MaxIsotopeError"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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62 <userParam value="As written in the spectrum or CID if no info" name="FragmentMethod"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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63 <userParam value="LowRes" name="Instrument"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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64 <userParam value="NoProtocol" name="Protocol"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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65 <userParam value="1" name="NumTolerableTermini"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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66 <userParam value="1" name="NumMatchesPerSpec"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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67 <userParam value="6" name="MinPepLength"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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68 <userParam value="40" name="MaxPepLength"/> |
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69 <userParam value="2" name="MinCharge"/> |
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70 <userParam value="3" name="MaxCharge"/> |
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71 </AdditionalSearchParams> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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72 <ModificationParams> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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73 <SearchModification residues="C" massDelta="57.021465" fixedMod="true"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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74 <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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75 </SearchModification> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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76 </ModificationParams> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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77 <Enzymes> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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78 <Enzyme missedCleavages="1000" semiSpecific="true" id="Tryp"> |
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79 <EnzymeName> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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80 <cvParam accession="MS:1001251" cvRef="PSI-MS" name="Trypsin"/> |
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81 </EnzymeName> |
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82 </Enzyme> |
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83 </Enzymes> |
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84 <ParentTolerance> |
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85 <cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="20.0" name="search tolerance plus value"/> |
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5a4801b7d106
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86 <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="20.0" name="search tolerance minus value"/> |
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5a4801b7d106
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87 </ParentTolerance> |
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88 <Threshold> |
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89 <cvParam accession="MS:1001494" cvRef="PSI-MS" name="no threshold"/> |
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90 </Threshold> |
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91 </SpectrumIdentificationProtocol> |
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92 </AnalysisProtocolCollection> |
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93 <DataCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1"> |
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94 <Inputs> |
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95 <SearchDatabase numDatabaseSequences="10" location="C:\cygwin\home\kims336\Data\SkylineDemo\Abbreviated.fasta" id="SearchDB_1"> |
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96 <FileFormat> |
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97 <cvParam accession="MS:1001348" cvRef="PSI-MS" name="FASTA format"/> |
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98 </FileFormat> |
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99 <DatabaseName> |
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100 <userParam name="Abbreviated.fasta"/> |
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101 </DatabaseName> |
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102 <cvParam accession="MS:1001197" cvRef="PSI-MS" name="DB composition target+decoy"/> |
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103 <cvParam accession="MS:1001283" cvRef="PSI-MS" value="^XXX" name="decoy DB accession regexp"/> |
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104 <cvParam accession="MS:1001195" cvRef="PSI-MS" name="decoy DB type reverse"/> |
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105 </SearchDatabase> |
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106 <SpectraData location="msgf-test.mzML" name="msgf-test.mzML" id="SID_1"> |
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107 <FileFormat> |
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108 <cvParam accession="MS:1000584" cvRef="PSI-MS" name="mzML file"/> |
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109 </FileFormat> |
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110 <SpectrumIDFormat> |
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111 <cvParam accession="MS:1000768" cvRef="PSI-MS" name="Thermo nativeID format"/> |
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112 </SpectrumIDFormat> |
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113 </SpectraData> |
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114 </Inputs> |
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115 <AnalysisData> |
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116 <SpectrumIdentificationList id="SI_LIST_1"> |
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117 <FragmentationTable> |
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118 <Measure id="Measure_MZ"> |
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119 <cvParam accession="MS:1001225" cvRef="PSI-MS" unitCvRef="PSI-MS" unitName="m/z" unitAccession="MS:1000040" name="product ion m/z"/> |
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120 </Measure> |
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121 </FragmentationTable> |
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122 <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10073" id="SIR_3"> |
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123 <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep1" calculatedMassToCharge="784.87060546875" experimentalMassToCharge="784.8652954101562" chargeState="2" id="SII_3_1"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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124 <PeptideEvidenceRef peptideEvidence_ref="PepEv_543_1_543"/> |
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125 <cvParam accession="MS:1002049" cvRef="PSI-MS" value="173" name="MS-GF:RawScore"/> |
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126 <cvParam accession="MS:1002050" cvRef="PSI-MS" value="228" name="MS-GF:DeNovoScore"/> |
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127 <cvParam accession="MS:1002052" cvRef="PSI-MS" value="3.3660747E-14" name="MS-GF:SpecEValue"/> |
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128 <cvParam accession="MS:1002053" cvRef="PSI-MS" value="1.6083104E-10" name="MS-GF:EValue"/> |
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129 <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/> |
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130 <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/> |
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131 <userParam value="0" name="IsotopeError"/> |
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132 <userParam value="CID" name="AssumedDissociationMethod"/> |
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133 </SpectrumIdentificationItem> |
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134 <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10073" name="scan number(s)"/> |
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135 </SpectrumIdentificationResult> |
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136 <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10075" id="SIR_5"> |
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137 <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep1" calculatedMassToCharge="523.5828247070312" experimentalMassToCharge="523.5802001953125" chargeState="3" id="SII_5_1"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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138 <PeptideEvidenceRef peptideEvidence_ref="PepEv_543_1_543"/> |
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139 <cvParam accession="MS:1002049" cvRef="PSI-MS" value="81" name="MS-GF:RawScore"/> |
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140 <cvParam accession="MS:1002050" cvRef="PSI-MS" value="104" name="MS-GF:DeNovoScore"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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141 <cvParam accession="MS:1002052" cvRef="PSI-MS" value="1.2290536E-12" name="MS-GF:SpecEValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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142 <cvParam accession="MS:1002053" cvRef="PSI-MS" value="5.8724186E-9" name="MS-GF:EValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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143 <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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144 <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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145 <userParam value="0" name="IsotopeError"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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146 <userParam value="CID" name="AssumedDissociationMethod"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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147 </SpectrumIdentificationItem> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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148 <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10075" name="scan number(s)"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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149 </SpectrumIdentificationResult> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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150 <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10071" id="SIR_1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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151 <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep2" calculatedMassToCharge="709.3224487304688" experimentalMassToCharge="709.3134765625" chargeState="2" id="SII_1_1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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152 <PeptideEvidenceRef peptideEvidence_ref="PepEv_901_2_165"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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153 <cvParam accession="MS:1002049" cvRef="PSI-MS" value="50" name="MS-GF:RawScore"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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154 <cvParam accession="MS:1002050" cvRef="PSI-MS" value="114" name="MS-GF:DeNovoScore"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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155 <cvParam accession="MS:1002052" cvRef="PSI-MS" value="9.0045643E-10" name="MS-GF:SpecEValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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156 <cvParam accession="MS:1002053" cvRef="PSI-MS" value="4.3023806E-6" name="MS-GF:EValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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157 <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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158 <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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159 <userParam value="0" name="IsotopeError"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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160 <userParam value="CID" name="AssumedDissociationMethod"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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161 </SpectrumIdentificationItem> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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162 <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10071" name="scan number(s)"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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163 </SpectrumIdentificationResult> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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164 <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10074" id="SIR_4"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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165 <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep3" calculatedMassToCharge="792.1166381835938" experimentalMassToCharge="792.4600219726562" chargeState="3" id="SII_4_1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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166 <PeptideEvidenceRef peptideEvidence_ref="PepEv_2320_3_327"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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167 <cvParam accession="MS:1002049" cvRef="PSI-MS" value="25" name="MS-GF:RawScore"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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168 <cvParam accession="MS:1002050" cvRef="PSI-MS" value="123" name="MS-GF:DeNovoScore"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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169 <cvParam accession="MS:1002052" cvRef="PSI-MS" value="4.4064498E-7" name="MS-GF:SpecEValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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170 <cvParam accession="MS:1002053" cvRef="PSI-MS" value="0.0021054016" name="MS-GF:EValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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171 <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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172 <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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173 <userParam value="1" name="IsotopeError"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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174 <userParam value="CID" name="AssumedDissociationMethod"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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175 </SpectrumIdentificationItem> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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176 <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10074" name="scan number(s)"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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177 </SpectrumIdentificationResult> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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178 <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="controllerType=0 controllerNumber=1 scan=10072" id="SIR_2"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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179 <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep4" calculatedMassToCharge="403.2303771972656" experimentalMassToCharge="403.7300109863281" chargeState="2" id="SII_2_1"> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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180 <PeptideEvidenceRef peptideEvidence_ref="PepEv_1960_4_156"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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181 <cvParam accession="MS:1002049" cvRef="PSI-MS" value="27" name="MS-GF:RawScore"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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182 <cvParam accession="MS:1002050" cvRef="PSI-MS" value="50" name="MS-GF:DeNovoScore"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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183 <cvParam accession="MS:1002052" cvRef="PSI-MS" value="1.4847345E-6" name="MS-GF:SpecEValue"/> |
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5a4801b7d106
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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184 <cvParam accession="MS:1002053" cvRef="PSI-MS" value="0.0070940615" name="MS-GF:EValue"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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185 <cvParam accession="MS:1002054" cvRef="PSI-MS" value="0.0" name="MS-GF:QValue"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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186 <cvParam accession="MS:1002055" cvRef="PSI-MS" value="0.0" name="MS-GF:PepQValue"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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187 <userParam value="1" name="IsotopeError"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
galaxyp
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188 <userParam value="CID" name="AssumedDissociationMethod"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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189 </SpectrumIdentificationItem> |
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190 <cvParam accession="MS:1001115" cvRef="PSI-MS" value="10072" name="scan number(s)"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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191 </SpectrumIdentificationResult> |
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192 </SpectrumIdentificationList> |
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193 </AnalysisData> |
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194 </DataCollection> |
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195 </MzIdentML> |