diff test-data/peak_detection3.imzml @ 3:c42549f04fdd draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
author galaxyp
date Fri, 15 Feb 2019 10:14:01 -0500
parents
children 4bd085117204
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peak_detection3.imzml	Fri Feb 15 10:14:01 2019 -0500
@@ -0,0 +1,324 @@
+<?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="{00515efe-60d8-4171-bb57-6f33c159ef7d}"/>
+   <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="59e17ebe18b0559646ba7a17e709054397f086ea"/>
+   <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/tmpPJKhfc/job_working_directory/000/8/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="0.11.5"/>
+ </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="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="38">
+    <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="304.595254080636" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" 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="38"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
+      <binary/>
+     </binaryDataArray>
+     <binaryDataArray encodedLength="0">
+      <referenceableParamGroupRef ref="intensityArray"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="320"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
+      <binary/>
+     </binaryDataArray>
+    </binaryDataArrayList>
+   </spectrum>
+   <spectrum index="1" id="Spectrum=2" defaultArrayLength="33">
+    <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="306.32292175293" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" 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="624"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
+      <binary/>
+     </binaryDataArray>
+     <binaryDataArray encodedLength="0">
+      <referenceableParamGroupRef ref="intensityArray"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="888"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
+      <binary/>
+     </binaryDataArray>
+    </binaryDataArrayList>
+   </spectrum>
+   <spectrum index="2" id="Spectrum=3" defaultArrayLength="28">
+    <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="328.937515258789" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="396.916674804687" 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="1152"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
+      <binary/>
+     </binaryDataArray>
+     <binaryDataArray encodedLength="0">
+      <referenceableParamGroupRef ref="intensityArray"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1376"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
+      <binary/>
+     </binaryDataArray>
+    </binaryDataArrayList>
+   </spectrum>
+   <spectrum index="3" id="Spectrum=4" defaultArrayLength="38">
+    <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="304.595254080636" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" 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="1600"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
+      <binary/>
+     </binaryDataArray>
+     <binaryDataArray encodedLength="0">
+      <referenceableParamGroupRef ref="intensityArray"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1904"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
+      <binary/>
+     </binaryDataArray>
+    </binaryDataArrayList>
+   </spectrum>
+   <spectrum index="4" id="Spectrum=5" defaultArrayLength="33">
+    <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="306.32292175293" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" 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="2208"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
+      <binary/>
+     </binaryDataArray>
+     <binaryDataArray encodedLength="0">
+      <referenceableParamGroupRef ref="intensityArray"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="2472"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
+      <binary/>
+     </binaryDataArray>
+    </binaryDataArrayList>
+   </spectrum>
+   <spectrum index="5" id="Spectrum=6" defaultArrayLength="28">
+    <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="328.937515258789" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="396.916674804687" 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="2736"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
+      <binary/>
+     </binaryDataArray>
+     <binaryDataArray encodedLength="0">
+      <referenceableParamGroupRef ref="intensityArray"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="2960"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
+      <binary/>
+     </binaryDataArray>
+    </binaryDataArrayList>
+   </spectrum>
+   <spectrum index="6" id="Spectrum=7" defaultArrayLength="38">
+    <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="304.595254080636" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" 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="3184"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
+      <binary/>
+     </binaryDataArray>
+     <binaryDataArray encodedLength="0">
+      <referenceableParamGroupRef ref="intensityArray"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="3488"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
+      <binary/>
+     </binaryDataArray>
+    </binaryDataArrayList>
+   </spectrum>
+   <spectrum index="7" id="Spectrum=8" defaultArrayLength="33">
+    <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="306.32292175293" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" 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="3792"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
+      <binary/>
+     </binaryDataArray>
+     <binaryDataArray encodedLength="0">
+      <referenceableParamGroupRef ref="intensityArray"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4056"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
+      <binary/>
+     </binaryDataArray>
+    </binaryDataArrayList>
+   </spectrum>
+   <spectrum index="8" id="Spectrum=9" defaultArrayLength="28">
+    <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="328.937515258789" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="396.916674804687" 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="4320"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
+      <binary/>
+     </binaryDataArray>
+     <binaryDataArray encodedLength="0">
+      <referenceableParamGroupRef ref="intensityArray"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4544"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
+      <binary/>
+     </binaryDataArray>
+    </binaryDataArrayList>
+   </spectrum>
+  </spectrumList>
+ </run>
+</mzML>