comparison test-data/small-index-filter.mzML @ 10:9d5de24e6ef7 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292

9:dd4ba10d0c45

<?xml version="1.0" encoding="utf-8"?>
<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
  <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="small" version="1.1.0">
    <cvList count="2">
      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
      <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
    </cvList>
    <fileDescription>
      <fileContent>
        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
      </fileContent>
      <sourceFileList count="3">
        <sourceFile id="RAW1" name="small.RAW" location="file:///C:\pwiz-src\trunk\pwiz\example_data">
          <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
          <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>
          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>
        </sourceFile>
        <sourceFile id="small.mzML" name="small.mzML" location="file:///">
          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>
        </sourceFile>
        <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">
          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>
        </sourceFile>
      </sourceFileList>
    </fileDescription>
    <referenceableParamGroupList count="1">
      <referenceableParamGroup id="CommonInstrumentParams">
        <cvParam cvRef="MS" accession="MS:1000448" name="LTQ FT" value=""/>
        <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>
      </referenceableParamGroup>
    </referenceableParamGroupList>
    <softwareList count="3">
      <software id="Xcalibur" version="1.1 Beta 7">
        <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
      </software>
      <software id="pwiz" version="3.0.8981">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
      </software>
      <software id="pwiz_3.0.8990" version="3.0.8990">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
      </software>
    </softwareList>
    <instrumentConfigurationList count="2">
      <instrumentConfiguration id="IC1">

        <processingMethod order="0" softwareRef="pwiz">
          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        </processingMethod>
      </dataProcessing>
      <dataProcessing id="pwiz_Reader_conversion">
        <processingMethod order="0" softwareRef="pwiz_3.0.8990">
          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        </processingMethod>
        <processingMethod order="1" softwareRef="pwiz_3.0.8990">
          <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
        </processingMethod>
      </dataProcessing>
    </dataProcessingList>
    <run id="small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2005-07-20T14:44:22Z" defaultSourceFileRef="RAW1">

      </chromatogramList>
    </run>
  </mzML>
  <indexList count="2">
    <index name="spectrum">
      <offset idRef="controllerType=0 controllerNumber=1 scan=3">5577</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=4">14148</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=5">26006</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=11">36522</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=14">47993</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=15">57476</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=16">65257</offset>
    </index>
    <index name="chromatogram">
      <offset idRef="TIC">76395</offset>
    </index>
  </indexList>
  <indexListOffset>78345</indexListOffset>
  <fileChecksum>0d5bbd9cad4ad9471eba2e80d0ddea2cddcf3db9</fileChecksum>
</indexedmzML>

10:9d5de24e6ef7

<?xml version="1.0" encoding="utf-8"?>
<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
  <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="small" version="1.1.0">
    <cvList count="2">
      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
      <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>
    </cvList>
    <fileDescription>
      <fileContent>
        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
      </fileContent>
      <sourceFileList count="3">
        <sourceFile id="RAW1" name="small.RAW" location="file:///">
          <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
          <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>
          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>
        </sourceFile>
        <sourceFile id="small.mzML" name="small.mzML" location="file:///">
          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>
        </sourceFile>
        <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">
          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>
        </sourceFile>
      </sourceFileList>
    </fileDescription>
    <referenceableParamGroupList count="1">
      <referenceableParamGroup id="CommonInstrumentParams">
        <cvParam cvRef="MS" accession="MS:1000448" name="LTQ FT" value=""/>
        <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>
      </referenceableParamGroup>
    </referenceableParamGroupList>
    <softwareList count="4">
      <software id="Xcalibur" version="1.1 Beta 7">
        <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
      </software>
      <software id="pwiz" version="3.0.8981">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
      </software>
      <software id="pwiz_3.0.19038" version="3.0.19038">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
      </software>
      <software id="pwiz_3.0.19044" version="3.0.19044">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
      </software>
    </softwareList>
    <instrumentConfigurationList count="2">
      <instrumentConfiguration id="IC1">

        <processingMethod order="0" softwareRef="pwiz">
          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        </processingMethod>
      </dataProcessing>
      <dataProcessing id="pwiz_Reader_conversion">
        <processingMethod order="0" softwareRef="pwiz_3.0.19038">
          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        </processingMethod>
        <processingMethod order="1" softwareRef="pwiz_3.0.19038">
          <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
        </processingMethod>
      </dataProcessing>
    </dataProcessingList>
    <run id="small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2005-07-20T14:44:22Z" defaultSourceFileRef="RAW1">

      </chromatogramList>
    </run>
  </mzML>
  <indexList count="2">
    <index name="spectrum">
      <offset idRef="controllerType=0 controllerNumber=1 scan=3">5697</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=4">14268</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=5">26126</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=11">36642</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=14">48113</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=15">57596</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=16">65377</offset>
    </index>
    <index name="chromatogram">
      <offset idRef="TIC">76515</offset>
    </index>
  </indexList>
  <indexListOffset>78465</indexListOffset>
  <fileChecksum>0671bee5b37c6f8cc8afde991309fd96af7f5c3d</fileChecksum>
</indexedmzML>