Mercurial > repos > galaxyp > openms_idfileconverter
diff test-data/SequenceCoverageCalculator.idXML @ 9:83cf7a4cd03c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
| author | galaxyp |
|---|---|
| date | Fri, 17 May 2019 04:51:22 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SequenceCoverageCalculator.idXML Fri May 17 04:51:22 2019 -0400 @@ -0,0 +1,161 @@ +<?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" 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<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" 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<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>