view test-data/outfile2.imzml @ 4:e9300ef37403 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
author galaxyp
date Fri, 22 Mar 2019 08:26:23 -0400
parents 36d38d2cf88c
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="{54a5519e-643b-4eb1-b82b-d55aaa5e9015}"/>
   <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="12d68eada8b274b1bba9520cef0ff98d6fc95bf4"/>
   <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous"/>
   <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/>
  </fileContent>
 </fileDescription>
 <softwareList count="1">
  <software id="MALDIquantForeign" version="0.11.5"/>
 </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="1"/>
   <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="100" 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="2" defaultDataProcessingRef="export">
   <spectrum index="0" id="scan=0" defaultArrayLength="8399">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="100.000007629395" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="799.816687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="16.7431673605698"/>
    <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="16"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
   <spectrum index="1" id="scan=1" defaultArrayLength="8399">
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="100.083335876465" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="799.9" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
    <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="10.6534160746182"/>
    <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="16"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
      <binary/>
     </binaryDataArray>
     <binaryDataArray encodedLength="0">
      <referenceableParamGroupRef ref="intensityArray"/>
      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400"/>
      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
      <binary/>
     </binaryDataArray>
    </binaryDataArrayList>
   </spectrum>
  </spectrumList>
 </run>
</mzML>