comparison test-data/small-mzWindow.mzML @ 11:052798dd73dd draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"

10:06747cba5685

<?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=""/>

        </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">
      <spectrumList count="48" defaultDataProcessingRef="pwiz_Reader_conversion">

      </chromatogramList>
    </run>
  </mzML>
  <indexList count="2">
    <index name="spectrum">
      <offset idRef="controllerType=0 controllerNumber=1 scan=1">5698</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=2">10803</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=3">16052</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=4">22867</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=5">30556</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=6">38068</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=7">45469</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=8">52785</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=9">57841</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=10">62938</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=11">69978</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=12">77634</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=13">84854</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=14">92282</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=15">99710</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=16">105248</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=17">110535</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=18">117570</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=19">125204</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=20">132414</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=21">139830</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=22">147340</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=23">153015</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=24">157990</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=25">165107</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=26">172811</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=27">180124</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=28">187366</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=29">194912</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=30">200601</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=31">205895</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=32">213491</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=33">220626</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=34">228062</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=35">235183</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=36">240534</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=37">245703</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=38">252740</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=39">260528</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=40">267704</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=41">275238</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=42">282498</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=43">288120</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=44">293378</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=45">300495</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=46">308170</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=47">315421</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=48">322778</offset>
    </index>
    <index name="chromatogram">
      <offset idRef="TIC">330136</offset>
    </index>
  </indexList>
  <indexListOffset>332086</indexListOffset>
  <fileChecksum>4c52055cc16e42e05ef5a8eae5df244ea6ead1ac</fileChecksum>
</indexedmzML>

11:052798dd73dd

<?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="4.1.41" 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=""/>

        </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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
        </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_3.0.20287" version="3.0.20287">
        <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_3.0.20287">
          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        </processingMethod>
        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
          <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
          <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
        </processingMethod>
      </dataProcessing>
    </dataProcessingList>
    <run id="small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2005-07-20T14:44:22Z" defaultSourceFileRef="RAW1">
      <spectrumList count="48" defaultDataProcessingRef="pwiz_Reader_conversion">

      </chromatogramList>
    </run>
  </mzML>
  <indexList count="2">
    <index name="spectrum">
      <offset idRef="controllerType=0 controllerNumber=1 scan=1">5614</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=2">10719</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=3">15968</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=4">22783</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=5">30472</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=6">37984</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=7">45385</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=8">52701</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=9">57757</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=10">62854</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=11">69894</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=12">77550</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=13">84770</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=14">92198</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=15">99626</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=16">105164</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=17">110451</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=18">117486</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=19">125120</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=20">132330</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=21">139746</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=22">147256</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=23">152931</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=24">157906</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=25">165023</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=26">172727</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=27">180040</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=28">187282</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=29">194828</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=30">200517</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=31">205811</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=32">213407</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=33">220542</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=34">227978</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=35">235099</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=36">240450</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=37">245619</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=38">252656</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=39">260444</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=40">267620</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=41">275154</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=42">282414</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=43">288036</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=44">293294</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=45">300411</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=46">308086</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=47">315337</offset>
      <offset idRef="controllerType=0 controllerNumber=1 scan=48">322694</offset>
    </index>
    <index name="chromatogram">
      <offset idRef="TIC">330052</offset>
    </index>
  </indexList>
  <indexListOffset>332002</indexListOffset>
  <fileChecksum>c854b1b0a8acbad401bff243741e2b6e87b59921</fileChecksum>
</indexedmzML>