comparison test-data/BrukerBafTest.mzML @ 10:9d5de24e6ef7 draft

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

10:9d5de24e6ef7

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      <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=""/>
      </fileContent>
      <sourceFileList count="1">
        <sourceFile id="BrukerBafTest.d_x005c_Analysis.baf" name="Analysis.baf" location="file:///">
          <cvParam cvRef="MS" accession="MS:1000772" name="Bruker BAF nativeID format" value=""/>
          <cvParam cvRef="MS" accession="MS:1000815" name="Bruker BAF format" value=""/>
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        <cvParam cvRef="MS" accession="MS:1001556" name="Bruker Daltonics apex series" value=""/>
      </referenceableParamGroup>
    </referenceableParamGroupList>
    <softwareList count="3">
      <software id="BAF2SQL" version="2.7.300.20-112">
        <cvParam cvRef="MS" accession="MS:1000692" name="Bruker software" value=""/>
        <userParam name="software name" value="BAF2SQL"/>
      </software>
      <software id="apexControl" version="ApexControl 3.0.0.alpha.35 (development version, April 18, 2008)">
        <cvParam cvRef="MS" accession="MS:1000706" name="apexControl" value=""/>
      </software>
      <software id="pwiz_Reader_Bruker" version="3.0.19044">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
      </software>
    </softwareList>
    <instrumentConfigurationList count="1">
      <instrumentConfiguration id="IC1">
        <referenceableParamGroupRef ref="CommonInstrumentParams"/>
        <componentList count="3">
          <source order="1">
            <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
            <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/>
          </source>
          <analyzer order="2">
            <cvParam cvRef="MS" accession="MS:1000079" name="fourier transform ion cyclotron resonance mass spectrometer" value=""/>
          </analyzer>
          <detector order="3">
            <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>
          </detector>
        </componentList>
        <softwareRef ref="apexControl"/>
      </instrumentConfiguration>
    </instrumentConfigurationList>
    <dataProcessingList count="1">
      <dataProcessing id="pwiz_Reader_Bruker_conversion">
        <processingMethod order="0" softwareRef="pwiz_Reader_Bruker">
          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        </processingMethod>
        <processingMethod order="1" softwareRef="pwiz_Reader_Bruker">
          <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
          <userParam name="Bruker/Agilent/CompassXtract peak picking"/>
        </processingMethod>
      </dataProcessing>
    </dataProcessingList>
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      <spectrumList count="1" defaultDataProcessingRef="pwiz_Reader_Bruker_conversion">
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          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="5.704013312e09"/>
          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
          <scanList count="1">
            <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
            <scan>
              <scanWindowList count="1">
                <scanWindow>
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            </scan>
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    </run>
  </mzML>
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    <index name="spectrum">
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    </index>
    <index name="chromatogram">
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