Mercurial > repos > galaxyp > maldi_quant_preprocessing

view test-data/peak_detection3.imzml @ 4:60ee8c592b13 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
author galaxyp
date Sat, 04 Mar 2023 19:14:31 +0000
parents 71411ac28268
children
line wrap: on
line source

<?xml version="1.0" encoding="utf-8"?>
<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="out" version="1.1.0">
 <cvList count="2">
  <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.44.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
  <cv id="UO" fullName="Unit Ontology" version="12:10:2012" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
  <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>
 </cvList>
 <fileDescription>
  <fileContent>
   <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
   <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{dfd6eff6-f7b3-46ec-bf1e-bbb5223f935b}"/>
   <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1abaedcd2dfe09f9c9c758e03f93a9df0bf815d3"/>
   <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
   <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/>
  </fileContent>
  <sourceFileList count="1">
   <sourceFile id="SF1" location="/tmp/tmp7arrd4fa/job_working_directory/000/14/working" name="infile.imzML">
    <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="0d2ad51f69d7b5df0f4d2b2a47b17478f2fca509"/>
   </sourceFile>
  </sourceFileList>
 </fileDescription>
 <softwareList count="1">
  <software id="MALDIquantForeign" version="0.13"/>
 </softwareList>
 <referenceableParamGroupList count="2">
  <referenceableParamGroup id="mzArray">
   <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
   <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
   <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
   <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
  </referenceableParamGroup>
  <referenceableParamGroup id="intensityArray">
   <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
   <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
   <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
   <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
  </referenceableParamGroup>
 </referenceableParamGroupList>
 <scanSettingsList count="1">
  <scanSettings id="scansetting1">
   <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3"/>
   <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3"/>
   <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
   <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
   <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
   <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
  </scanSettings>
 </scanSettingsList>
 <instrumentConfigurationList count="1">
  <instrumentConfiguration id="IC0"/>
 </instrumentConfigurationList>
 <dataProcessingList count="1">
  <dataProcessing id="export">
   <processingMethod order="1" softwareRef="MALDIquantForeign">
    <userParam name="MALDIquant object(s) exported to mzML" value=""/>
   </processingMethod>
  </dataProcessing>
 </dataProcessingList>
 <run id="run0" defaultInstrumentConfigurationRef="IC0">
  <spectrumList count="9" defaultDataProcessingRef="export">
   <spectrum index="0" id="Spectrum=1" defaultArrayLength="9">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="304.166687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="9"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="72"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="88"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="9"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="72"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="1" id="Spectrum=2" defaultArrayLength="16">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="300.25" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="378.75" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="160"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="16"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="128"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="288"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="16"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="128"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="2" id="Spectrum=3" defaultArrayLength="17">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="304.666687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="398.166687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="416"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="136"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="552"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="136"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="3" id="Spectrum=4" defaultArrayLength="14">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="302.833343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="398.75" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="688"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="14"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="112"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="800"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="14"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="112"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="4" id="Spectrum=5" defaultArrayLength="12">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="300.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="383.166687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="912"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="12"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="96"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1008"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="12"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="96"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="5" id="Spectrum=6" defaultArrayLength="10">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="324.5" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="392" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1104"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="80"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1184"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="80"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="6" id="Spectrum=7" defaultArrayLength="13">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="305" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="366.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1264"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="104"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1368"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="104"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="7" id="Spectrum=8" defaultArrayLength="17">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="304.666687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="393.583343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1472"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="136"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1608"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="136"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="8" id="Spectrum=9" defaultArrayLength="14">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="304" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="394.833343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
    <scanList count="1">
     <scan>
      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
     </scan>
    </scanList>
    <binaryDataArrayList count="2">
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="mzArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1744"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="14"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="112"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1856"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="14"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="112"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
  </spectrumList>
 </run>
</mzML>