Mercurial > repos > galaxyp > msconvert

comparison test-data/small-index-filter.mzML @ 15:6153e8ada1ee draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
author galaxyp
date Mon, 30 Nov 2020 16:01:10 +0000
parents 9d5de24e6ef7
children
comparison
equal deleted inserted replaced
14:3cf310697624 15:6153e8ada1ee
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="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/> 5 <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.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"/> 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>
10 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/> 10 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
18 </sourceFile> 18 </sourceFile>
19 <sourceFile id="small.mzML" name="small.mzML" location="file:///"> 19 <sourceFile id="small.mzML" name="small.mzML" location="file:///">
20 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/> 20 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>
21 </sourceFile> 21 </sourceFile>
22 <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///"> 22 <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">
23 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/> 23 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
24 </sourceFile> 24 </sourceFile>
25 </sourceFileList> 25 </sourceFileList>
26 </fileDescription> 26 </fileDescription>
27 <referenceableParamGroupList count="1"> 27 <referenceableParamGroupList count="1">
28 <referenceableParamGroup id="CommonInstrumentParams"> 28 <referenceableParamGroup id="CommonInstrumentParams">
29 <cvParam cvRef="MS" accession="MS:1000448" name="LTQ FT" value=""/> 29 <cvParam cvRef="MS" accession="MS:1000448" name="LTQ FT" value=""/>
30 <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/> 30 <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>
31 </referenceableParamGroup> 31 </referenceableParamGroup>
32 </referenceableParamGroupList> 32 </referenceableParamGroupList>
33 <softwareList count="4"> 33 <softwareList count="3">
34 <software id="Xcalibur" version="1.1 Beta 7"> 34 <software id="Xcalibur" version="1.1 Beta 7">
35 <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/> 35 <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
36 </software> 36 </software>
37 <software id="pwiz" version="3.0.8981"> 37 <software id="pwiz" version="3.0.8981">
38 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> 38 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
39 </software> 39 </software>
40 <software id="pwiz_3.0.19038" version="3.0.19038"> 40 <software id="pwiz_3.0.20287" version="3.0.20287">
41 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
42 </software>
43 <software id="pwiz_3.0.19044" version="3.0.19044">
44 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> 41 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
45 </software> 42 </software>
46 </softwareList> 43 </softwareList>
47 <instrumentConfigurationList count="2"> 44 <instrumentConfigurationList count="2">
48 <instrumentConfiguration id="IC1"> 45 <instrumentConfiguration id="IC1">
83 <processingMethod order="0" softwareRef="pwiz"> 80 <processingMethod order="0" softwareRef="pwiz">
84 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> 81 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
85 </processingMethod> 82 </processingMethod>
86 </dataProcessing> 83 </dataProcessing>
87 <dataProcessing id="pwiz_Reader_conversion"> 84 <dataProcessing id="pwiz_Reader_conversion">
88 <processingMethod order="0" softwareRef="pwiz_3.0.19038"> 85 <processingMethod order="0" softwareRef="pwiz_3.0.20287">
89 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> 86 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
90 </processingMethod> 87 </processingMethod>
91 <processingMethod order="1" softwareRef="pwiz_3.0.19038"> 88 <processingMethod order="1" softwareRef="pwiz_3.0.20287">
92 <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/> 89 <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
90 <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
93 </processingMethod> 91 </processingMethod>
94 </dataProcessing> 92 </dataProcessing>
95 </dataProcessingList> 93 </dataProcessingList>
96 <run id="small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2005-07-20T14:44:22Z" defaultSourceFileRef="RAW1"> 94 <run id="small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2005-07-20T14:44:22Z" defaultSourceFileRef="RAW1">
97 <spectrumList count="7" defaultDataProcessingRef="pwiz_Reader_conversion"> 95 <spectrumList count="7" defaultDataProcessingRef="pwiz_Reader_conversion">
497 </chromatogramList> 495 </chromatogramList>
498 </run> 496 </run>
499 </mzML> 497 </mzML>
500 <indexList count="2"> 498 <indexList count="2">
501 <index name="spectrum"> 499 <index name="spectrum">
502 <offset idRef="controllerType=0 controllerNumber=1 scan=3">5697</offset> 500 <offset idRef="controllerType=0 controllerNumber=1 scan=3">5613</offset>
503 <offset idRef="controllerType=0 controllerNumber=1 scan=4">14268</offset> 501 <offset idRef="controllerType=0 controllerNumber=1 scan=4">14184</offset>
504 <offset idRef="controllerType=0 controllerNumber=1 scan=5">26126</offset> 502 <offset idRef="controllerType=0 controllerNumber=1 scan=5">26042</offset>
505 <offset idRef="controllerType=0 controllerNumber=1 scan=11">36642</offset> 503 <offset idRef="controllerType=0 controllerNumber=1 scan=11">36558</offset>
506 <offset idRef="controllerType=0 controllerNumber=1 scan=14">48113</offset> 504 <offset idRef="controllerType=0 controllerNumber=1 scan=14">48029</offset>
507 <offset idRef="controllerType=0 controllerNumber=1 scan=15">57596</offset> 505 <offset idRef="controllerType=0 controllerNumber=1 scan=15">57512</offset>
508 <offset idRef="controllerType=0 controllerNumber=1 scan=16">65377</offset> 506 <offset idRef="controllerType=0 controllerNumber=1 scan=16">65293</offset>
509 </index> 507 </index>
510 <index name="chromatogram"> 508 <index name="chromatogram">
511 <offset idRef="TIC">76515</offset> 509 <offset idRef="TIC">76431</offset>
512 </index> 510 </index>
513 </indexList> 511 </indexList>
514 <indexListOffset>78465</indexListOffset> 512 <indexListOffset>78381</indexListOffset>
515 <fileChecksum>0671bee5b37c6f8cc8afde991309fd96af7f5c3d</fileChecksum> 513 <fileChecksum>190e7438359420dfb1a9b11d5829700a34ec36bd</fileChecksum>
516 </indexedmzML> 514 </indexedmzML>