Mercurial > repos > galaxyp > openms_peakpickerwavelet
view test-data/SequenceCoverageCalculator.idXML @ 7:17913dee7f88 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
| author | galaxyp |
|---|---|
| date | Wed, 15 May 2019 08:31:10 -0400 |
| parents | |
| children |
line wrap: on
line source
<?xml version="1.0" encoding="UTF-8"?> <?xml-stylesheet type="text/xsl" href="https://www.openms.de/xml-stylesheet/IdXML.xsl" ?> <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"> <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" > <UserParam type="string" name="input_consensusXML" value="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.consensusXML"/> <UserParam type="string" name="input_mzML" value="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.mzML"/> <UserParam type="string" name="input_decoys" value=""/> <UserParam type="int" name="decoy_prefix" value="0"/> <UserParam type="string" name="decoy_string" value="decoy"/> <UserParam type="string" name="out_xquest_specxml" value="OpenPepXL_output.spec.xml.tmp"/> <UserParam type="int" name="precursor:min_charge" value="3"/> <UserParam type="int" name="precursor:max_charge" value="7"/> <UserParam type="float" name="fragment:mass_tolerance_xlinks" value="0.3"/> <UserParam type="int" name="peptide:min_size" value="5"/> <UserParam type="stringList" name="cross_link:residue1" value="[K]"/> <UserParam type="stringList" name="cross_link:residue2" value="[K]"/> <UserParam type="float" name="cross_link:mass" value="138.0680796"/> <UserParam type="float" name="cross_link:mass_isoshift" value="12.075321"/> <UserParam type="floatList" name="cross_link:mass_monolink" value="[156.07864431, 155.094628715]"/> <UserParam type="string" name="cross_link:name" value="DSS"/> <UserParam type="int" name="modifications:variable_max_per_peptide" value="2"/> <UserParam type="int" name="MS:1001029" value="329"/> </SearchParameters> <IdentificationRun date="2018-03-06T13:21:04" search_engine="OpenXQuest" search_engine_version="2.3.0" search_parameters_ref="SP_0" > <ProteinIdentification score_type="" higher_score_better="true" significance_threshold="0" > <ProteinHit id="PH_0" accession="Protein3" score="0" sequence="" > <UserParam type="string" name="target_decoy" value="target"/> </ProteinHit> <ProteinHit id="PH_1" accession="Protein2" score="0" sequence="" > <UserParam type="string" name="target_decoy" value="target"/> </ProteinHit> <ProteinHit id="PH_2" accession="Protein1" score="0" sequence="" > <UserParam type="string" name="target_decoy" value="target"/> </ProteinHit> <UserParam type="string" name="SpectrumIdentificationProtocol" value="MS:1002494"/> </ProteinIdentification> <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" > <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" > <UserParam type="string" name="fragment_annotation" value="1004.99096679688,0.334201395511627,2,"[alpha|xi$b18]""/> <UserParam type="string" name="spectrum_reference" value="spectrum=99"/> <UserParam type="string" name="target_decoy" value="target"/> <UserParam type="int" name="spectrum_index" value="81"/> <UserParam type="float" name="xl_mass" value="156.07864431"/> <UserParam type="string" name="xl_chain" value="MS:1002509"/> <UserParam type="int" name="xl_pos" value="15"/> <UserParam type="string" name="xl_type" value="mono-link"/> <UserParam type="int" name="xl_rank" value="2"/> <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/> <UserParam type="float" name="spec_heavy_RT" value="2099.09545898438"/> <UserParam type="float" name="spec_heavy_MZ" value="732.436096191406"/> <UserParam type="string" name="spectrum_reference_heavy" value="spectrum=48"/> <UserParam type="int" name="spectrum_index_heavy" value="39"/> <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="-3.29631082786707"/> <UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.000333623265276995"/> <UserParam type="float" name="OpenXQuest:xcorr common" value="-0.0259976562688046"/> <UserParam type="float" name="OpenXQuest:match-odds" value="0.00212489435959964"/> <UserParam type="float" name="OpenXQuest:intsum" value="0.334201395511627"/> <UserParam type="float" name="OpenXQuest:wTIC" value="0.0688459236181392"/> <UserParam type="float" name="OpenXQuest:TIC" value="0.0688459236181392"/> <UserParam type="float" name="OpenXQuest:prescore" value="0.00694444449618459"/> <UserParam type="float" name="OpenXQuest:log_occupancy" value="0.0564614974779924"/> <UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="0.0564614974779924"/> <UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/> <UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="0.0231329371940407"/> <UserParam type="float" name="HyperCommon" value="0"/> <UserParam type="float" name="HyperXlink" value="0.288332907246581"/> <UserParam type="float" name="HyperAlpha" value="2.58943363761124"/> <UserParam type="float" name="HyperBeta" value="0"/> <UserParam type="float" name="HyperBoth" value="2.58943363761124"/> <UserParam type="int" name="matched_xlink_alpha" value="1"/> <UserParam type="int" name="matched_xlink_beta" value="0"/> <UserParam type="int" name="matched_common_alpha" value="0"/> <UserParam type="int" name="matched_common_beta" value="0"/> <UserParam type="string" name="selected" value="false"/> <UserParam type="string" name="protein_references" value="unique"/> </PeptideHit> </PeptideIdentification> <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" > <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" > <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]""/> <UserParam type="string" name="spectrum_reference" value="spectrum=123"/> <UserParam type="string" name="target_decoy" value="target"/> <UserParam type="int" name="spectrum_index" value="101"/> <UserParam type="float" name="xl_mass" value="156.07864431"/> <UserParam type="string" name="xl_chain" value="MS:1002509"/> <UserParam type="int" name="xl_pos" value="5"/> <UserParam type="string" name="xl_type" value="mono-link"/> <UserParam type="int" name="xl_rank" value="1"/> <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/> <UserParam type="float" name="spec_heavy_RT" value="2110.98901367188"/> <UserParam type="float" name="spec_heavy_MZ" value="471.971282958984"/> <UserParam type="string" name="spectrum_reference_heavy" value="spectrum=77"/> <UserParam type="int" name="spectrum_index_heavy" value="63"/> <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="0.735970556846563"/> <UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.237457299396362"/> <UserParam type="float" name="OpenXQuest:xcorr common" value="0.529048564861274"/> <UserParam type="float" name="OpenXQuest:match-odds" value="1.3649637673649"/> <UserParam type="float" name="OpenXQuest:intsum" value="2.92258863151073"/> <UserParam type="float" name="OpenXQuest:wTIC" value="0.660300024858228"/> <UserParam type="float" name="OpenXQuest:TIC" value="0.660300024858228"/> <UserParam type="float" name="OpenXQuest:prescore" value="0.0795454531908035"/> <UserParam type="float" name="OpenXQuest:log_occupancy" value="3.16483711801473"/> <UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="3.16483711801473"/> <UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/> <UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="2.33666522248801"/> <UserParam type="float" name="HyperCommon" value="5.59770114368979"/> <UserParam type="float" name="HyperXlink" value="4.32762764114041"/> <UserParam type="float" name="HyperAlpha" value="11.9960758128656"/> <UserParam type="float" name="HyperBeta" value="0"/> <UserParam type="float" name="HyperBoth" value="11.9960758128656"/> <UserParam type="int" name="matched_xlink_alpha" value="3"/> <UserParam type="int" name="matched_xlink_beta" value="0"/> <UserParam type="int" name="matched_common_alpha" value="4"/> <UserParam type="int" name="matched_common_beta" value="0"/> <UserParam type="string" name="selected" value="false"/> <UserParam type="string" name="protein_references" value="unique"/> </PeptideHit> </PeptideIdentification> <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" > <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" > <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]""/> <UserParam type="string" name="spectrum_reference" value="spectrum=238"/> <UserParam type="string" name="target_decoy" value="target"/> <UserParam type="int" name="spectrum_index" value="195"/> <UserParam type="float" name="xl_mass" value="156.07864431"/> <UserParam type="string" name="xl_chain" value="MS:1002509"/> <UserParam type="int" name="xl_pos" value="7"/> <UserParam type="string" name="xl_type" value="mono-link"/> <UserParam type="int" name="xl_rank" value="1"/> <UserParam type="string" name="xl_term_spec" value="ANYWHERE"/> <UserParam type="float" name="spec_heavy_RT" value="2221.23388666232"/> <UserParam type="float" name="spec_heavy_MZ" value="660.072448730469"/> <UserParam type="string" name="spectrum_reference_heavy" value="spectrum=219"/> <UserParam type="int" name="spectrum_index_heavy" value="180"/> <UserParam type="float" name="OMS:precursor_mz_error_ppm" value="6.2016465793789"/> <UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.389891893192958"/> <UserParam type="float" name="OpenXQuest:xcorr common" value="0.462351176037813"/> <UserParam type="float" name="OpenXQuest:match-odds" value="2.59304858228082"/> <UserParam type="float" name="OpenXQuest:intsum" value="3.03074353560805"/> <UserParam type="float" name="OpenXQuest:wTIC" value="0.672367841921044"/> <UserParam type="float" name="OpenXQuest:TIC" value="0.672367841921044"/> <UserParam type="float" name="OpenXQuest:prescore" value="0.107142858207226"/> <UserParam type="float" name="OpenXQuest:log_occupancy" value="5.62904796479063"/> <UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="5.62904796479063"/> <UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/> <UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="5.33167976719043"/> <UserParam type="float" name="HyperCommon" value="8.15707933298946"/> <UserParam type="float" name="HyperXlink" value="4.59543196178458"/> <UserParam type="float" name="HyperAlpha" value="17.3945020752073"/> <UserParam type="float" name="HyperBeta" value="0"/> <UserParam type="float" name="HyperBoth" value="17.3945020752073"/> <UserParam type="int" name="matched_xlink_alpha" value="5"/> <UserParam type="int" name="matched_xlink_beta" value="0"/> <UserParam type="int" name="matched_common_alpha" value="7"/> <UserParam type="int" name="matched_common_beta" value="0"/> <UserParam type="string" name="selected" value="false"/> <UserParam type="string" name="protein_references" value="unique"/> </PeptideHit> </PeptideIdentification> </IdentificationRun> </IdXML>