Mercurial > repos > galaxyp > openms_fuzzydiff
annotate test-data/SequenceCoverageCalculator.idXML @ 9:42b3646bc300 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
| author | galaxyp |
|---|---|
| date | Wed, 15 May 2019 08:02:13 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
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9
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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1 <?xml version="1.0" encoding="UTF-8"?> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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2 <?xml-stylesheet type="text/xsl" href="https://www.openms.de/xml-stylesheet/IdXML.xsl" ?> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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3 <IdXML version="1.5" xsi:noNamespaceSchemaLocation="https://www.openms.de/xml-schema/IdXML_1_5.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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4 <SearchParameters id="SP_0" db="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="3,4,5,6,7" enzyme="trypsin" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="0.2" peak_mass_tolerance_ppm="false" > |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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5 <UserParam type="string" name="input_consensusXML" value="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.consensusXML"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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6 <UserParam type="string" name="input_mzML" value="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.mzML"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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7 <UserParam type="string" name="input_decoys" value=""/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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8 <UserParam type="int" name="decoy_prefix" value="0"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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9 <UserParam type="string" name="decoy_string" value="decoy"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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10 <UserParam type="string" name="out_xquest_specxml" value="OpenPepXL_output.spec.xml.tmp"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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11 <UserParam type="int" name="precursor:min_charge" value="3"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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12 <UserParam type="int" name="precursor:max_charge" value="7"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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13 <UserParam type="float" name="fragment:mass_tolerance_xlinks" value="0.3"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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14 <UserParam type="int" name="peptide:min_size" value="5"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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15 <UserParam type="stringList" name="cross_link:residue1" value="[K]"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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16 <UserParam type="stringList" name="cross_link:residue2" value="[K]"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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17 <UserParam type="float" name="cross_link:mass" value="138.0680796"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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18 <UserParam type="float" name="cross_link:mass_isoshift" value="12.075321"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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19 <UserParam type="floatList" name="cross_link:mass_monolink" value="[156.07864431, 155.094628715]"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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20 <UserParam type="string" name="cross_link:name" value="DSS"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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21 <UserParam type="int" name="modifications:variable_max_per_peptide" value="2"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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22 <UserParam type="int" name="MS:1001029" value="329"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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23 </SearchParameters> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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24 <IdentificationRun date="2018-03-06T13:21:04" search_engine="OpenXQuest" search_engine_version="2.3.0" search_parameters_ref="SP_0" > |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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25 <ProteinIdentification score_type="" higher_score_better="true" significance_threshold="0" > |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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26 <ProteinHit id="PH_0" accession="Protein3" score="0" sequence="" > |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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27 <UserParam type="string" name="target_decoy" value="target"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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changeset
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28 </ProteinHit> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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29 <ProteinHit id="PH_1" accession="Protein2" score="0" sequence="" > |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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30 <UserParam type="string" name="target_decoy" value="target"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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31 </ProteinHit> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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32 <ProteinHit id="PH_2" accession="Protein1" score="0" sequence="" > |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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33 <UserParam type="string" name="target_decoy" value="target"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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34 </ProteinHit> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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35 <UserParam type="string" name="SpectrumIdentificationProtocol" value="MS:1002494"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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changeset
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36 </ProteinIdentification> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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37 <PeptideIdentification score_type="OpenXQuest:combined score" higher_score_better="true" significance_threshold="0" MZ="728.411010742188" RT="2120.05249023438" spectrum_reference="spectrum=99,spectrum=48" > |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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38 <PeptideHit score="0.936605209529642" sequence="LAAPQLVQMFIGDGAK(Xlink:DSS)LVR" charge="3" aa_before="K" aa_after="D" start="249" end="267" protein_refs="PH_1" > |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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changeset
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39 <UserParam type="string" name="fragment_annotation" value="1004.99096679688,0.334201395511627,2,"[alpha|xi$b18]""/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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40 <UserParam type="string" name="spectrum_reference" value="spectrum=99"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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41 <UserParam type="string" name="target_decoy" value="target"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
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42 <UserParam type="int" name="spectrum_index" value="81"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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changeset
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43 <UserParam type="float" name="xl_mass" value="156.07864431"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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44 <UserParam type="string" name="xl_chain" value="MS:1002509"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
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45 <UserParam type="int" name="xl_pos" value="15"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
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46 <UserParam type="string" name="xl_type" value="mono-link"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
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47 <UserParam type="int" name="xl_rank" value="2"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
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48 <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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49 <UserParam type="float" name="spec_heavy_RT" value="2099.09545898438"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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50 <UserParam type="float" name="spec_heavy_MZ" value="732.436096191406"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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51 <UserParam type="string" name="spectrum_reference_heavy" value="spectrum=48"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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52 <UserParam type="int" name="spectrum_index_heavy" value="39"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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53 <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="-3.29631082786707"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
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54 <UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.000333623265276995"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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55 <UserParam type="float" name="OpenXQuest:xcorr common" value="-0.0259976562688046"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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56 <UserParam type="float" name="OpenXQuest:match-odds" value="0.00212489435959964"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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57 <UserParam type="float" name="OpenXQuest:intsum" value="0.334201395511627"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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58 <UserParam type="float" name="OpenXQuest:wTIC" value="0.0688459236181392"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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59 <UserParam type="float" name="OpenXQuest:TIC" value="0.0688459236181392"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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60 <UserParam type="float" name="OpenXQuest:prescore" value="0.00694444449618459"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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61 <UserParam type="float" name="OpenXQuest:log_occupancy" value="0.0564614974779924"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
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62 <UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="0.0564614974779924"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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63 <UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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64 <UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="0.0231329371940407"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
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65 <UserParam type="float" name="HyperCommon" value="0"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
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66 <UserParam type="float" name="HyperXlink" value="0.288332907246581"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
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67 <UserParam type="float" name="HyperAlpha" value="2.58943363761124"/> |
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42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
68 <UserParam type="float" name="HyperBeta" value="0"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
69 <UserParam type="float" name="HyperBoth" value="2.58943363761124"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
70 <UserParam type="int" name="matched_xlink_alpha" value="1"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
71 <UserParam type="int" name="matched_xlink_beta" value="0"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
72 <UserParam type="int" name="matched_common_alpha" value="0"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
73 <UserParam type="int" name="matched_common_beta" value="0"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
74 <UserParam type="string" name="selected" value="false"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
75 <UserParam type="string" name="protein_references" value="unique"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
76 </PeptideHit> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
77 </PeptideIdentification> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
78 <PeptideIdentification score_type="OpenXQuest:combined score" higher_score_better="true" significance_threshold="0" MZ="467.945617675781" RT="2129.23608398438" spectrum_reference="spectrum=123,spectrum=77" > |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
79 <PeptideHit score="28.2731402412177" sequence="GGVHVK(Xlink:DSS)LAHLSK" charge="3" aa_before="R" aa_after="H" start="292" end="303" protein_refs="PH_0" > |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
80 <UserParam type="string" name="fragment_annotation" value="396.987884521484,0.384458035230637,3,"[alpha|xi$y9]"|449.323913574219,0.387931138277054,3,"[alpha|xi$y11]"|450.284820556641,0.393777251243591,1,"[alpha|ci$b5]"|484.207611083984,0.215591758489609,1,"[alpha|ci$y4]"|555.274353027344,0.297201305627823,1,"[alpha|ci$y5]"|595.053527832031,1,2,"[alpha|xi$y9]"|668.345275878906,0.243629142642021,1,"[alpha|ci$y6]""/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
81 <UserParam type="string" name="spectrum_reference" value="spectrum=123"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
82 <UserParam type="string" name="target_decoy" value="target"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
83 <UserParam type="int" name="spectrum_index" value="101"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
84 <UserParam type="float" name="xl_mass" value="156.07864431"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
85 <UserParam type="string" name="xl_chain" value="MS:1002509"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
86 <UserParam type="int" name="xl_pos" value="5"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
87 <UserParam type="string" name="xl_type" value="mono-link"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
88 <UserParam type="int" name="xl_rank" value="1"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
89 <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
90 <UserParam type="float" name="spec_heavy_RT" value="2110.98901367188"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
91 <UserParam type="float" name="spec_heavy_MZ" value="471.971282958984"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
92 <UserParam type="string" name="spectrum_reference_heavy" value="spectrum=77"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
93 <UserParam type="int" name="spectrum_index_heavy" value="63"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
94 <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="0.735970556846563"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
95 <UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.237457299396362"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
96 <UserParam type="float" name="OpenXQuest:xcorr common" value="0.529048564861274"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
97 <UserParam type="float" name="OpenXQuest:match-odds" value="1.3649637673649"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
98 <UserParam type="float" name="OpenXQuest:intsum" value="2.92258863151073"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
99 <UserParam type="float" name="OpenXQuest:wTIC" value="0.660300024858228"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
100 <UserParam type="float" name="OpenXQuest:TIC" value="0.660300024858228"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
101 <UserParam type="float" name="OpenXQuest:prescore" value="0.0795454531908035"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
102 <UserParam type="float" name="OpenXQuest:log_occupancy" value="3.16483711801473"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
103 <UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="3.16483711801473"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
104 <UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
105 <UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="2.33666522248801"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
106 <UserParam type="float" name="HyperCommon" value="5.59770114368979"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
107 <UserParam type="float" name="HyperXlink" value="4.32762764114041"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
108 <UserParam type="float" name="HyperAlpha" value="11.9960758128656"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
109 <UserParam type="float" name="HyperBeta" value="0"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
110 <UserParam type="float" name="HyperBoth" value="11.9960758128656"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
111 <UserParam type="int" name="matched_xlink_alpha" value="3"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
112 <UserParam type="int" name="matched_xlink_beta" value="0"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
113 <UserParam type="int" name="matched_common_alpha" value="4"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
114 <UserParam type="int" name="matched_common_beta" value="0"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
115 <UserParam type="string" name="selected" value="false"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
116 <UserParam type="string" name="protein_references" value="unique"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
117 </PeptideHit> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
118 </PeptideIdentification> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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119 <PeptideIdentification score_type="OpenXQuest:combined score" higher_score_better="true" significance_threshold="0" MZ="656.050903320313" RT="2228.50292963107" spectrum_reference="spectrum=238,spectrum=219" > |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
120 <PeptideHit score="30.0056519661123" sequence="EVIELPLK(Xlink:DSS)NPELFLR" charge="3" aa_before="R" aa_after="V" start="145" end="159" protein_refs="PH_2" > |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
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121 <UserParam type="string" name="fragment_annotation" value="387.815673828125,0.215708956122398,2,"[alpha|ci$y6]"|435.218322753906,0.0836383178830147,1,"[alpha|ci$y3]"|444.946411132812,0.119465403258801,2,"[alpha|ci$y7]"|471.207763671875,0.061412189155817,1,"[alpha|ci$b4]"|584.244018554688,0.203754380345345,1,"[alpha|ci$b5]"|692.068786621094,1,2,"[alpha|xi$y10]"|748.578674316406,0.292433172464371,2,"[alpha|xi$y11]"|774.424987792969,0.361789405345917,1,"[alpha|ci$y6]"|812.867004394531,0.152033895254135,2,"[alpha|xi$y12]"|839.981567382812,0.125570505857468,2,"[alpha|xi$b13]"|888.39013671875,0.356793075799942,1,"[alpha|ci$y7]"|896.316162109375,0.0581442341208458,2,"[alpha|xi$b14]""/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
122 <UserParam type="string" name="spectrum_reference" value="spectrum=238"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
123 <UserParam type="string" name="target_decoy" value="target"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
124 <UserParam type="int" name="spectrum_index" value="195"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
125 <UserParam type="float" name="xl_mass" value="156.07864431"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
126 <UserParam type="string" name="xl_chain" value="MS:1002509"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
127 <UserParam type="int" name="xl_pos" value="7"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
128 <UserParam type="string" name="xl_type" value="mono-link"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
129 <UserParam type="int" name="xl_rank" value="1"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
130 <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
131 <UserParam type="float" name="spec_heavy_RT" value="2221.23388666232"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
changeset
|
132 <UserParam type="float" name="spec_heavy_MZ" value="660.072448730469"/> |
|
42b3646bc300
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
diff
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133 <UserParam type="string" name="spectrum_reference_heavy" value="spectrum=219"/> |
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134 <UserParam type="int" name="spectrum_index_heavy" value="180"/> |
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135 <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="6.2016465793789"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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136 <UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.389891893192958"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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137 <UserParam type="float" name="OpenXQuest:xcorr common" value="0.462351176037813"/> |
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42b3646bc300
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138 <UserParam type="float" name="OpenXQuest:match-odds" value="2.59304858228082"/> |
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139 <UserParam type="float" name="OpenXQuest:intsum" value="3.03074353560805"/> |
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140 <UserParam type="float" name="OpenXQuest:wTIC" value="0.672367841921044"/> |
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141 <UserParam type="float" name="OpenXQuest:TIC" value="0.672367841921044"/> |
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142 <UserParam type="float" name="OpenXQuest:prescore" value="0.107142858207226"/> |
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143 <UserParam type="float" name="OpenXQuest:log_occupancy" value="5.62904796479063"/> |
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144 <UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="5.62904796479063"/> |
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145 <UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/> |
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146 <UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="5.33167976719043"/> |
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147 <UserParam type="float" name="HyperCommon" value="8.15707933298946"/> |
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148 <UserParam type="float" name="HyperXlink" value="4.59543196178458"/> |
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149 <UserParam type="float" name="HyperAlpha" value="17.3945020752073"/> |
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150 <UserParam type="float" name="HyperBeta" value="0"/> |
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151 <UserParam type="float" name="HyperBoth" value="17.3945020752073"/> |
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152 <UserParam type="int" name="matched_xlink_alpha" value="5"/> |
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153 <UserParam type="int" name="matched_xlink_beta" value="0"/> |
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154 <UserParam type="int" name="matched_common_alpha" value="7"/> |
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155 <UserParam type="int" name="matched_common_beta" value="0"/> |
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156 <UserParam type="string" name="selected" value="false"/> |
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157 <UserParam type="string" name="protein_references" value="unique"/> |
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158 </PeptideHit> |
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159 </PeptideIdentification> |
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160 </IdentificationRun> |
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161 </IdXML> |