Mercurial > repos > galaxyp > msconvert

comparison test-data/small-denoise.mzML @ 10:9d5de24e6ef7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
author galaxyp
date Sat, 23 Feb 2019 06:25:48 -0500
parents dd4ba10d0c45
children 6153e8ada1ee
comparison
equal deleted inserted replaced
9:dd4ba10d0c45 10:9d5de24e6ef7
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <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"> 2 <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">
3 <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"> 3 <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">
4 <cvList count="2"> 4 <cvList count="2">
5 <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/> 5 <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"/>
6 <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/> 6 <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>
7 </cvList> 7 </cvList>
8 <fileDescription> 8 <fileDescription>
9 <fileContent> 9 <fileContent>
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11 <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/> 11 <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
12 </fileContent> 12 </fileContent>
13 <sourceFileList count="3"> 13 <sourceFileList count="3">
14 <sourceFile id="RAW1" name="small.RAW" location="file:///C:\pwiz-src\trunk\pwiz\example_data"> 14 <sourceFile id="RAW1" name="small.RAW" location="file:///">
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18 </sourceFile> 18 </sourceFile>
19 <sourceFile id="small.mzML" name="small.mzML" location="file:///"> 19 <sourceFile id="small.mzML" name="small.mzML" location="file:///">
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31 </referenceableParamGroup> 31 </referenceableParamGroup>
32 </referenceableParamGroupList> 32 </referenceableParamGroupList>
33 <softwareList count="3"> 33 <softwareList count="4">
34 <software id="Xcalibur" version="1.1 Beta 7"> 34 <software id="Xcalibur" version="1.1 Beta 7">
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36 </software> 36 </software>
37 <software id="pwiz" version="3.0.8981"> 37 <software id="pwiz" version="3.0.8981">
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42 </software>
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42 </software> 45 </software>
43 </softwareList> 46 </softwareList>
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82 </processingMethod> 85 </processingMethod>
83 </dataProcessing> 86 </dataProcessing>
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92 </dataProcessingList> 95 </dataProcessingList>
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1970 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/> 1973 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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1973 </binaryDataArrayList> 1976 </binaryDataArrayList>
1974 </spectrum> 1977 </spectrum>
1975 <spectrum index="35" id="controllerType=0 controllerNumber=1 scan=36" defaultArrayLength="732" dataProcessingRef="pwiz_Reader_conversion"> 1978 <spectrum index="35" id="controllerType=0 controllerNumber=1 scan=36" defaultArrayLength="731" dataProcessingRef="pwiz_Reader_conversion">
1976 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/> 1979 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
1977 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/> 1980 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
1978 <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/> 1981 <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
1979 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/> 1982 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
1980 <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="810.545532226563" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> 1983 <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="810.545532226563" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
1996 </scanWindow> 1999 </scanWindow>
1997 </scanWindowList> 2000 </scanWindowList>
1998 </scan> 2001 </scan>
1999 </scanList> 2002 </scanList>
2000 <binaryDataArrayList count="2"> 2003 <binaryDataArrayList count="2">
2001 <binaryDataArray encodedLength="3496"> 2004 <binaryDataArray encodedLength="3488">
2002 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/> 2005 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
2003 <cvParam cvRef="MS" accession="MS:1002312" name="MS-Numpress linear prediction compression" value=""/> 2006 <cvParam cvRef="MS" accession="MS:1002312" name="MS-Numpress linear prediction compression" value=""/>
2004 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> 2007 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
2005 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