Mercurial > repos > galaxyp > maldi_quant_preprocessing

diff test-data/outfile2.imzml @ 3:71411ac28268 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
author galaxyp
date Fri, 15 Feb 2019 10:26:00 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outfile2.imzml	Fri Feb 15 10:26:00 2019 -0500
@@ -0,0 +1,118 @@
+<?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">
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+  <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"/>
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+  <referenceableParamGroup id="intensityArray">
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+   <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">
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+   <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3"/>
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+   <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">
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+    <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="16.7431673605698"/>
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+      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
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+    </scanList>
+    <binaryDataArrayList count="2">
+     <binaryDataArray encodedLength="0">
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+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
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+      <binary/>
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+     <binaryDataArray encodedLength="0">
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+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
+      <binary/>
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+   </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"/>
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+    <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="10.6534160746182"/>
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+      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
+     </scan>
+    </scanList>
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+      <binary/>
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+  </spectrumList>
+ </run>
+</mzML>