view test-data/small-peakpicking-cwt-allMS.mzML @ 2:c1287690a62c draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 532424dd138aa77ec59704fb5680f5ed0e2195f3

<?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="4.0.1" 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="2">
        <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>
      </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_3.0.9987" version="3.0.9987">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
      </software>
    </softwareList>
    <instrumentConfigurationList count="2">
      <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="Xcalibur"/>
      </instrumentConfiguration>
      <instrumentConfiguration id="IC2">
        <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:1000083" name="radial ejection linear ion trap" value=""/>
          </analyzer>
          <detector order="3">
            <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>
          </detector>
        </componentList>
        <softwareRef ref="Xcalibur"/>
      </instrumentConfiguration>
    </instrumentConfigurationList>
    <dataProcessingList count="2">
      <dataProcessing id="pwiz_Reader_Thermo_conversion">
        <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_3.0.9987">
          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        </processingMethod>
        <processingMethod order="1" softwareRef="pwiz_3.0.9987">
          <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">
      <spectrumList count="48" defaultDataProcessingRef="pwiz_Reader_conversion">
        <spectrum index="0" id="controllerType=0 controllerNumber=1 scan=1" defaultArrayLength="723" dataProcessingRef="pwiz_Reader_conversion">
          <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
          <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
          <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
          <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="810.415283203125" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
          <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="1.471973875e06" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1.5245068e07"/>
          <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="200.00018816645" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
          <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="2000.009946620377" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
          <scanList count="1">
            <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
            <scan>
              <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="0.004935" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
              <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="FTMS + p ESI Full ms [200.00-2000.00]"/>
              <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="1"/>
              <cvParam cvRef="MS" accession="MS:1000927" name="ion injection time" value="68.227485656738" unitCvRef="UO" unitAccession="UO:0000028" unitName="millisecond"/>
              <scanWindowList count="1">
                <scanWindow>
                  <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="200.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                  <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                </scanWindow>
              </scanWindowList>
            </scan>
          </scanList>
          <binaryDataArrayList count="2">
            <binaryDataArray encodedLength="7248">
              <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
              <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
              <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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