Mercurial > repos > galaxyp > openms_rnpxl
comparison test-data/SequenceCoverageCalculator.idXML @ 8:4dbfc881d14f draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty
| author | galaxyp |
|---|---|
| date | Fri, 17 May 2019 09:26:40 -0400 |
| parents | 49d8333edbfb |
| children |
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| 7:49d8333edbfb | 8:4dbfc881d14f |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <?xml-stylesheet type="text/xsl" href="https://www.openms.de/xml-stylesheet/IdXML.xsl" ?> | |
| 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"> | |
| 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" > | |
| 5 <UserParam type="string" name="input_consensusXML" value="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.consensusXML"/> | |
| 6 <UserParam type="string" name="input_mzML" value="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.mzML"/> | |
| 7 <UserParam type="string" name="input_decoys" value=""/> | |
| 8 <UserParam type="int" name="decoy_prefix" value="0"/> | |
| 9 <UserParam type="string" name="decoy_string" value="decoy"/> | |
| 10 <UserParam type="string" name="out_xquest_specxml" value="OpenPepXL_output.spec.xml.tmp"/> | |
| 11 <UserParam type="int" name="precursor:min_charge" value="3"/> | |
| 12 <UserParam type="int" name="precursor:max_charge" value="7"/> | |
| 13 <UserParam type="float" name="fragment:mass_tolerance_xlinks" value="0.3"/> | |
| 14 <UserParam type="int" name="peptide:min_size" value="5"/> | |
| 15 <UserParam type="stringList" name="cross_link:residue1" value="[K]"/> | |
| 16 <UserParam type="stringList" name="cross_link:residue2" value="[K]"/> | |
| 17 <UserParam type="float" name="cross_link:mass" value="138.0680796"/> | |
| 18 <UserParam type="float" name="cross_link:mass_isoshift" value="12.075321"/> | |
| 19 <UserParam type="floatList" name="cross_link:mass_monolink" value="[156.07864431, 155.094628715]"/> | |
| 20 <UserParam type="string" name="cross_link:name" value="DSS"/> | |
| 21 <UserParam type="int" name="modifications:variable_max_per_peptide" value="2"/> | |
| 22 <UserParam type="int" name="MS:1001029" value="329"/> | |
| 23 </SearchParameters> | |
| 24 <IdentificationRun date="2018-03-06T13:21:04" search_engine="OpenXQuest" search_engine_version="2.3.0" search_parameters_ref="SP_0" > | |
| 25 <ProteinIdentification score_type="" higher_score_better="true" significance_threshold="0" > | |
| 26 <ProteinHit id="PH_0" accession="Protein3" score="0" sequence="" > | |
| 27 <UserParam type="string" name="target_decoy" value="target"/> | |
| 28 </ProteinHit> | |
| 29 <ProteinHit id="PH_1" accession="Protein2" score="0" sequence="" > | |
| 30 <UserParam type="string" name="target_decoy" value="target"/> | |
| 31 </ProteinHit> | |
| 32 <ProteinHit id="PH_2" accession="Protein1" score="0" sequence="" > | |
| 33 <UserParam type="string" name="target_decoy" value="target"/> | |
| 34 </ProteinHit> | |
| 35 <UserParam type="string" name="SpectrumIdentificationProtocol" value="MS:1002494"/> | |
| 36 </ProteinIdentification> | |
| 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" > | |
| 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" > | |
| 39 <UserParam type="string" name="fragment_annotation" value="1004.99096679688,0.334201395511627,2,"[alpha|xi$b18]""/> | |
| 40 <UserParam type="string" name="spectrum_reference" value="spectrum=99"/> | |
| 41 <UserParam type="string" name="target_decoy" value="target"/> | |
| 42 <UserParam type="int" name="spectrum_index" value="81"/> | |
| 43 <UserParam type="float" name="xl_mass" value="156.07864431"/> | |
| 44 <UserParam type="string" name="xl_chain" value="MS:1002509"/> | |
| 45 <UserParam type="int" name="xl_pos" value="15"/> | |
| 46 <UserParam type="string" name="xl_type" value="mono-link"/> | |
| 47 <UserParam type="int" name="xl_rank" value="2"/> | |
| 48 <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/> | |
| 49 <UserParam type="float" name="spec_heavy_RT" value="2099.09545898438"/> | |
| 50 <UserParam type="float" name="spec_heavy_MZ" value="732.436096191406"/> | |
| 51 <UserParam type="string" name="spectrum_reference_heavy" value="spectrum=48"/> | |
| 52 <UserParam type="int" name="spectrum_index_heavy" value="39"/> | |
| 53 <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="-3.29631082786707"/> | |
| 54 <UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.000333623265276995"/> | |
| 55 <UserParam type="float" name="OpenXQuest:xcorr common" value="-0.0259976562688046"/> | |
| 56 <UserParam type="float" name="OpenXQuest:match-odds" value="0.00212489435959964"/> | |
| 57 <UserParam type="float" name="OpenXQuest:intsum" value="0.334201395511627"/> | |
| 58 <UserParam type="float" name="OpenXQuest:wTIC" value="0.0688459236181392"/> | |
| 59 <UserParam type="float" name="OpenXQuest:TIC" value="0.0688459236181392"/> | |
| 60 <UserParam type="float" name="OpenXQuest:prescore" value="0.00694444449618459"/> | |
| 61 <UserParam type="float" name="OpenXQuest:log_occupancy" value="0.0564614974779924"/> | |
| 62 <UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="0.0564614974779924"/> | |
| 63 <UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/> | |
| 64 <UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="0.0231329371940407"/> | |
| 65 <UserParam type="float" name="HyperCommon" value="0"/> | |
| 66 <UserParam type="float" name="HyperXlink" value="0.288332907246581"/> | |
| 67 <UserParam type="float" name="HyperAlpha" value="2.58943363761124"/> | |
| 68 <UserParam type="float" name="HyperBeta" value="0"/> | |
| 69 <UserParam type="float" name="HyperBoth" value="2.58943363761124"/> | |
| 70 <UserParam type="int" name="matched_xlink_alpha" value="1"/> | |
| 71 <UserParam type="int" name="matched_xlink_beta" value="0"/> | |
| 72 <UserParam type="int" name="matched_common_alpha" value="0"/> | |
| 73 <UserParam type="int" name="matched_common_beta" value="0"/> | |
| 74 <UserParam type="string" name="selected" value="false"/> | |
| 75 <UserParam type="string" name="protein_references" value="unique"/> | |
| 76 </PeptideHit> | |
| 77 </PeptideIdentification> | |
| 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" > | |
| 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" > | |
| 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]""/> | |
| 81 <UserParam type="string" name="spectrum_reference" value="spectrum=123"/> | |
| 82 <UserParam type="string" name="target_decoy" value="target"/> | |
| 83 <UserParam type="int" name="spectrum_index" value="101"/> | |
| 84 <UserParam type="float" name="xl_mass" value="156.07864431"/> | |
| 85 <UserParam type="string" name="xl_chain" value="MS:1002509"/> | |
| 86 <UserParam type="int" name="xl_pos" value="5"/> | |
| 87 <UserParam type="string" name="xl_type" value="mono-link"/> | |
| 88 <UserParam type="int" name="xl_rank" value="1"/> | |
| 89 <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/> | |
| 90 <UserParam type="float" name="spec_heavy_RT" value="2110.98901367188"/> | |
| 91 <UserParam type="float" name="spec_heavy_MZ" value="471.971282958984"/> | |
| 92 <UserParam type="string" name="spectrum_reference_heavy" value="spectrum=77"/> | |
| 93 <UserParam type="int" name="spectrum_index_heavy" value="63"/> | |
| 94 <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="0.735970556846563"/> | |
| 95 <UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.237457299396362"/> | |
| 96 <UserParam type="float" name="OpenXQuest:xcorr common" value="0.529048564861274"/> | |
| 97 <UserParam type="float" name="OpenXQuest:match-odds" value="1.3649637673649"/> | |
| 98 <UserParam type="float" name="OpenXQuest:intsum" value="2.92258863151073"/> | |
| 99 <UserParam type="float" name="OpenXQuest:wTIC" value="0.660300024858228"/> | |
| 100 <UserParam type="float" name="OpenXQuest:TIC" value="0.660300024858228"/> | |
| 101 <UserParam type="float" name="OpenXQuest:prescore" value="0.0795454531908035"/> | |
| 102 <UserParam type="float" name="OpenXQuest:log_occupancy" value="3.16483711801473"/> | |
| 103 <UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="3.16483711801473"/> | |
| 104 <UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/> | |
| 105 <UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="2.33666522248801"/> | |
| 106 <UserParam type="float" name="HyperCommon" value="5.59770114368979"/> | |
| 107 <UserParam type="float" name="HyperXlink" value="4.32762764114041"/> | |
| 108 <UserParam type="float" name="HyperAlpha" value="11.9960758128656"/> | |
| 109 <UserParam type="float" name="HyperBeta" value="0"/> | |
| 110 <UserParam type="float" name="HyperBoth" value="11.9960758128656"/> | |
| 111 <UserParam type="int" name="matched_xlink_alpha" value="3"/> | |
| 112 <UserParam type="int" name="matched_xlink_beta" value="0"/> | |
| 113 <UserParam type="int" name="matched_common_alpha" value="4"/> | |
| 114 <UserParam type="int" name="matched_common_beta" value="0"/> | |
| 115 <UserParam type="string" name="selected" value="false"/> | |
| 116 <UserParam type="string" name="protein_references" value="unique"/> | |
| 117 </PeptideHit> | |
| 118 </PeptideIdentification> | |
| 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" > | |
| 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" > | |
| 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]""/> | |
| 122 <UserParam type="string" name="spectrum_reference" value="spectrum=238"/> | |
| 123 <UserParam type="string" name="target_decoy" value="target"/> | |
| 124 <UserParam type="int" name="spectrum_index" value="195"/> | |
| 125 <UserParam type="float" name="xl_mass" value="156.07864431"/> | |
| 126 <UserParam type="string" name="xl_chain" value="MS:1002509"/> | |
| 127 <UserParam type="int" name="xl_pos" value="7"/> | |
| 128 <UserParam type="string" name="xl_type" value="mono-link"/> | |
| 129 <UserParam type="int" name="xl_rank" value="1"/> | |
| 130 <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/> | |
| 131 <UserParam type="float" name="spec_heavy_RT" value="2221.23388666232"/> | |
| 132 <UserParam type="float" name="spec_heavy_MZ" value="660.072448730469"/> | |
| 133 <UserParam type="string" name="spectrum_reference_heavy" value="spectrum=219"/> | |
| 134 <UserParam type="int" name="spectrum_index_heavy" value="180"/> | |
| 135 <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="6.2016465793789"/> | |
| 136 <UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.389891893192958"/> | |
| 137 <UserParam type="float" name="OpenXQuest:xcorr common" value="0.462351176037813"/> | |
| 138 <UserParam type="float" name="OpenXQuest:match-odds" value="2.59304858228082"/> | |
| 139 <UserParam type="float" name="OpenXQuest:intsum" value="3.03074353560805"/> | |
| 140 <UserParam type="float" name="OpenXQuest:wTIC" value="0.672367841921044"/> | |
| 141 <UserParam type="float" name="OpenXQuest:TIC" value="0.672367841921044"/> | |
| 142 <UserParam type="float" name="OpenXQuest:prescore" value="0.107142858207226"/> | |
| 143 <UserParam type="float" name="OpenXQuest:log_occupancy" value="5.62904796479063"/> | |
| 144 <UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="5.62904796479063"/> | |
| 145 <UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/> | |
| 146 <UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="5.33167976719043"/> | |
| 147 <UserParam type="float" name="HyperCommon" value="8.15707933298946"/> | |
| 148 <UserParam type="float" name="HyperXlink" value="4.59543196178458"/> | |
| 149 <UserParam type="float" name="HyperAlpha" value="17.3945020752073"/> | |
| 150 <UserParam type="float" name="HyperBeta" value="0"/> | |
| 151 <UserParam type="float" name="HyperBoth" value="17.3945020752073"/> | |
| 152 <UserParam type="int" name="matched_xlink_alpha" value="5"/> | |
| 153 <UserParam type="int" name="matched_xlink_beta" value="0"/> | |
| 154 <UserParam type="int" name="matched_common_alpha" value="7"/> | |
| 155 <UserParam type="int" name="matched_common_beta" value="0"/> | |
| 156 <UserParam type="string" name="selected" value="false"/> | |
| 157 <UserParam type="string" name="protein_references" value="unique"/> | |
| 158 </PeptideHit> | |
| 159 </PeptideIdentification> | |
| 160 </IdentificationRun> | |
| 161 </IdXML> |