Mercurial > repos > galaxyp > idconvert
diff test-data/Rpal_01.pepXML @ 0:4f7d6bec667f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
| author | galaxyp |
|---|---|
| date | Fri, 08 Apr 2016 16:07:32 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Rpal_01.pepXML Fri Apr 08 16:07:32 2016 -0400 @@ -0,0 +1,49047 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<msms_pipeline_analysis date="2011-10-31T11:08:11" summary_xml="Rpal_01.pepXML" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd"> + <analysis_summary analysis="MyriMatch" version="2.1.101" time="2011-10-31T11:08:11"/> + <msms_run_summary base_name="Rpal_01" raw_data_type="" raw_data=""> + <sample_enzyme name="Trypsin/P" independent="false" fidelity="specific"> + <specificity sense="C" cut="KR" no_cut="" min_spacing="1"/> + </sample_enzyme> + <search_summary base_name="Rpal_01" search_engine="MyriMatch" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" out_data_type="" out_data=""> + <search_database local_path="Mark12-Rpal-20050929-reverse.fasta" database_name="SDB" type="AA"/> + <enzymatic_search_constraint enzyme="Trypsin/P" max_num_internal_cleavages="100000" min_number_termini="2"/> + <parameter name="Config: AvgPrecursorMzTolerance" value="1.5mz"/> + <parameter name="Config: ClassSizeMultiplier" value="2"/> + <parameter name="Config: CleavageRules" value="trypsin/p"/> + <parameter name="Config: ComputeXCorr" value="1"/> + <parameter name="Config: DecoyPrefix" value="rev_"/> + <parameter name="Config: DynamicMods" value=""/> + <parameter name="Config: EstimateSearchTimeOnly" value="0"/> + <parameter name="Config: FragmentMzTolerance" value="30ppm"/> + <parameter name="Config: FragmentationAutoRule" value="1"/> + <parameter name="Config: FragmentationRule" value="cid"/> + <parameter name="Config: MaxDynamicMods" value="2"/> + <parameter name="Config: MaxFragmentChargeState" value="0"/> + <parameter name="Config: MaxMissedCleavages" value="100000"/> + <parameter name="Config: MaxPeakCount" value="300"/> + <parameter name="Config: MaxPeptideLength" value="75"/> + <parameter name="Config: MaxPeptideMass" value="10000"/> + <parameter name="Config: MaxPeptideVariants" value="1000000"/> + <parameter name="Config: MaxResultRank" value="2"/> + <parameter name="Config: MinPeptideLength" value="5"/> + <parameter name="Config: MinPeptideMass" value="0"/> + <parameter name="Config: MinResultScore" value="9.9999999999999995e-008"/> + <parameter name="Config: MinTerminiCleavages" value="2"/> + <parameter name="Config: MonoPrecursorMzTolerance" value="10ppm"/> + <parameter name="Config: MonoisotopeAdjustmentSet" value="[-1,2] "/> + <parameter name="Config: NumBatches" value="50"/> + <parameter name="Config: NumChargeStates" value="3"/> + <parameter name="Config: NumIntensityClasses" value="3"/> + <parameter name="Config: NumMzFidelityClasses" value="3"/> + <parameter name="Config: OutputFormat" value="pepXML"/> + <parameter name="Config: OutputSuffix" value=""/> + <parameter name="Config: PrecursorMzToleranceRule" value="auto"/> + <parameter name="Config: PreferIntenseComplements" value="1"/> + <parameter name="Config: ProteinDatabase" value="Mark12-Rpal-20050929-reverse.fasta"/> + <parameter name="Config: ProteinListFilters" value=""/> + <parameter name="Config: ProteinSamplingTime" value="15"/> + <parameter name="Config: ResultsPerBatch" value="200000"/> + <parameter name="Config: SpectrumListFilters" value="peakPicking true 2-"/> + <parameter name="Config: StaticMods" value=""/> + <parameter name="Config: StatusUpdateFrequency" value="5"/> + <parameter name="Config: TicCutoffPercentage" value="0.97999999999999998"/> + <parameter name="Config: UseMultipleProcessors" value="1"/> + <parameter name="Config: UseSmartPlusThreeModel" value="1"/> + <parameter name="Config: WorkingDirectory" value="C:\test\rpal-orbi-orbi\raw"/> + <parameter name="PeakCounts: 1stQuartile: Filtered" value="94"/> + <parameter name="PeakCounts: 1stQuartile: Original" value="109"/> + <parameter name="PeakCounts: 2ndQuartile: Filtered" value="130"/> + <parameter name="PeakCounts: 2ndQuartile: Original" value="148"/> + <parameter name="PeakCounts: 3rdQuartile: Filtered" value="162"/> + <parameter name="PeakCounts: 3rdQuartile: Original" value="182"/> + <parameter name="PeakCounts: Mean: Filtered" value="127"/> + <parameter name="PeakCounts: Mean: Original" value="143"/> + <parameter name="PeakCounts: Min/Max: Filtered" value="9 / 299"/> + <parameter name="PeakCounts: Min/Max: Original" value="9 / 365"/> + <parameter name="SearchEngine: Name" value="MyriMatch"/> + <parameter name="SearchEngine: Version" value="2.1.101"/> + <parameter name="SearchStats: Nodes" value="1"/> + <parameter name="SearchStats: Overall" value="9696 proteins; 2367559 peptides; 1463799 variants; 1624470 comparisons"/> + <parameter name="SearchTime: Duration" value="18.9302578 seconds"/> + <parameter name="SearchTime: Started" value="11:07:52 on 10/31/2011"/> + <parameter name="SearchTime: Stopped" value="11:08:11 on 10/31/2011"/> + </search_summary> + <spectrum_query spectrum="Rpal_01.4.4.2" spectrumNativeID="controllerType=0 controllerNumber=1 scan=4" start_scan="4" end_scan="4" precursor_neutral_mass="971.24544706624" assumed_charge="2" index="2"> + <search_result num_target_comparisons="2774" num_decoy_comparisons="2735"> + <search_hit hit_rank="1" peptide="VMKNVIDR" peptide_prev_aa="R" peptide_next_aa="G" protein="rev_RPA0498" num_tot_proteins="1" calc_neutral_pep_mass="974.1791" massdiff="2.93365293376" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="1" tot_num_ions="14"> + <search_score name="number of matched peaks" value="1"/> + <search_score name="number of unmatched peaks" value="13"/> + <search_score name="mvh" value="5.705950021744"/> + <search_score name="mzFidelity" value="7.087171850592"/> + <search_score name="xcorr" value="0.12372587929479778"/> + </search_hit> + <search_hit hit_rank="2" peptide="RTTPLDLR" peptide_prev_aa="R" peptide_next_aa="R" protein="RPA1332" num_tot_proteins="1" calc_neutral_pep_mass="971.11226" massdiff="-0.13318706624" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="1" tot_num_ions="15"> + <search_score name="number of matched peaks" value="1"/> + <search_score name="number of unmatched peaks" value="14"/> + <search_score name="mvh" value="5.637738227844"/> + <search_score name="mzFidelity" value="6.950056555619"/> + <search_score name="xcorr" value="0.16826496059233614"/> + </search_hit> + <search_hit hit_rank="2" peptide="MYDFGSPR" peptide_prev_aa="K" peptide_next_aa="G" protein="rev_RPA3341" num_tot_proteins="1" calc_neutral_pep_mass="972.07534" massdiff="0.82989293376" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="1" tot_num_ions="15"> + <search_score name="number of matched peaks" value="1"/> + <search_score name="number of unmatched peaks" value="14"/> + <search_score name="mvh" value="5.637738227844"/> + <search_score name="mzFidelity" value="6.950056555619"/> + <search_score name="xcorr" value="0.24158960944600402"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="Rpal_01.4.4.3" spectrumNativeID="controllerType=0 controllerNumber=1 scan=4" start_scan="4" end_scan="4" precursor_neutral_mass="1456.86817059936" assumed_charge="3" index="3"> + <search_result num_target_comparisons="2774" num_decoy_comparisons="2735"> + <search_hit hit_rank="1" peptide="AAAEGERVLGFALR" peptide_prev_aa="R" peptide_next_aa="S" protein="RPA1259" num_tot_proteins="1" calc_neutral_pep_mass="1459.64904" massdiff="2.78086940064" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="2" tot_num_ions="27"> + <search_score name="number of matched peaks" value="2"/> + <search_score name="number of unmatched peaks" value="25"/> + <search_score name="mvh" value="9.639448642731"/> + <search_score name="mzFidelity" value="12.288225127384"/> + <search_score name="xcorr" value="0.24297397212008945"/> + </search_hit> + <search_hit 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