Mercurial > repos > galaxyp > msconvert

comparison test-data/small-ms-level-filter.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>
10 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/> 10 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
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:///">
15 <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/> 15 <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
16 <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/> 16 <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>
17 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/> 17 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>
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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/> 23 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>
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="3"> 33 <softwareList count="4">
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_3.0.8990" version="3.0.8990"> 40 <software id="pwiz_3.0.19038" version="3.0.19038">
41 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
42 </software>
43 <software id="pwiz_3.0.19044" version="3.0.19044">
41 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> 44 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
42 </software> 45 </software>
43 </softwareList> 46 </softwareList>
44 <instrumentConfigurationList count="2"> 47 <instrumentConfigurationList count="2">
45 <instrumentConfiguration id="IC1"> 48 <instrumentConfiguration id="IC1">
80 <processingMethod order="0" softwareRef="pwiz"> 83 <processingMethod order="0" softwareRef="pwiz">
81 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> 84 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
82 </processingMethod> 85 </processingMethod>
83 </dataProcessing> 86 </dataProcessing>
84 <dataProcessing id="pwiz_Reader_conversion"> 87 <dataProcessing id="pwiz_Reader_conversion">
85 <processingMethod order="0" softwareRef="pwiz_3.0.8990"> 88 <processingMethod order="0" softwareRef="pwiz_3.0.19038">
86 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> 89 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
87 </processingMethod> 90 </processingMethod>
88 <processingMethod order="1" softwareRef="pwiz_3.0.8990"> 91 <processingMethod order="1" softwareRef="pwiz_3.0.19038">
89 <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/> 92 <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
90 </processingMethod> 93 </processingMethod>
91 </dataProcessing> 94 </dataProcessing>
92 </dataProcessingList> 95 </dataProcessingList>
93 <run id="small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2005-07-20T14:44:22Z" defaultSourceFileRef="RAW1"> 96 <run id="small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2005-07-20T14:44:22Z" defaultSourceFileRef="RAW1">
2154 </chromatogramList> 2157 </chromatogramList>
2155 </run> 2158 </run>
2156 </mzML> 2159 </mzML>
2157 <indexList count="2"> 2160 <indexList count="2">
2158 <index name="spectrum"> 2161 <index name="spectrum">
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2193 </index> 2196 </index>
2194 <index name="chromatogram"> 2197 <index name="chromatogram">
2195 <offset idRef="TIC">347713</offset> 2198 <offset idRef="TIC">347833</offset>
2196 </index> 2199 </index>
2197 </indexList> 2200 </indexList>
2198 <indexListOffset>349663</indexListOffset> 2201 <indexListOffset>349783</indexListOffset>
2199 <fileChecksum>e47c8b99f8a38261a6a99445767638bda0d81200</fileChecksum> 2202 <fileChecksum>b37853cea35a8233460f48bc42abefd34f982729</fileChecksum>
2200 </indexedmzML> 2203 </indexedmzML>