Mercurial > repos > galaxyp > msconvert

comparison test-data/small-threshold.mzML @ 7:e638f7fad66a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
author galaxyp
date Sat, 23 Feb 2019 06:21:27 -0500
parents 6b6bba73eadb
children 052798dd73dd
comparison
equal deleted inserted replaced
6:6b6bba73eadb 7:e638f7fad66a
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="4.0.1" 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="2d5cdd239d18de37386cf9409e30693767b16f82"/> 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_3.0.9987" version="3.0.9987"> 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_3.0.9987"> 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_3.0.9987"> 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">
2714 </chromatogramList> 2717 </chromatogramList>
2715 </run> 2718 </run>
2716 </mzML> 2719 </mzML>
2717 <indexList count="2"> 2720 <indexList count="2">
2718 <index name="spectrum"> 2721 <index name="spectrum">
2719 <offset idRef="controllerType=0 controllerNumber=1 scan=1">5577</offset> 2722 <offset idRef="controllerType=0 controllerNumber=1 scan=1">5698</offset>
2720 <offset idRef="controllerType=0 controllerNumber=1 scan=2">9949</offset> 2723 <offset idRef="controllerType=0 controllerNumber=1 scan=2">10070</offset>
2721 <offset idRef="controllerType=0 controllerNumber=1 scan=3">14340</offset> 2724 <offset idRef="controllerType=0 controllerNumber=1 scan=3">14461</offset>
2722 <offset idRef="controllerType=0 controllerNumber=1 scan=4">20364</offset> 2725 <offset idRef="controllerType=0 controllerNumber=1 scan=4">20485</offset>
2723 <offset idRef="controllerType=0 controllerNumber=1 scan=5">26386</offset> 2726 <offset idRef="controllerType=0 controllerNumber=1 scan=5">26507</offset>
2724 <offset idRef="controllerType=0 controllerNumber=1 scan=6">32375</offset> 2727 <offset idRef="controllerType=0 controllerNumber=1 scan=6">32496</offset>
2725 <offset idRef="controllerType=0 controllerNumber=1 scan=7">38361</offset> 2728 <offset idRef="controllerType=0 controllerNumber=1 scan=7">38482</offset>
2726 <offset idRef="controllerType=0 controllerNumber=1 scan=8">44382</offset> 2729 <offset idRef="controllerType=0 controllerNumber=1 scan=8">44503</offset>
2727 <offset idRef="controllerType=0 controllerNumber=1 scan=9">48745</offset> 2730 <offset idRef="controllerType=0 controllerNumber=1 scan=9">48866</offset>
2728 <offset idRef="controllerType=0 controllerNumber=1 scan=10">53104</offset> 2731 <offset idRef="controllerType=0 controllerNumber=1 scan=10">53225</offset>
2729 <offset idRef="controllerType=0 controllerNumber=1 scan=11">59133</offset> 2732 <offset idRef="controllerType=0 controllerNumber=1 scan=11">59254</offset>
2730 <offset idRef="controllerType=0 controllerNumber=1 scan=12">65158</offset> 2733 <offset idRef="controllerType=0 controllerNumber=1 scan=12">65279</offset>
2731 <offset idRef="controllerType=0 controllerNumber=1 scan=13">71139</offset> 2734 <offset idRef="controllerType=0 controllerNumber=1 scan=13">71260</offset>
2732 <offset idRef="controllerType=0 controllerNumber=1 scan=14">77128</offset> 2735 <offset idRef="controllerType=0 controllerNumber=1 scan=14">77249</offset>
2733 <offset idRef="controllerType=0 controllerNumber=1 scan=15">83121</offset> 2736 <offset idRef="controllerType=0 controllerNumber=1 scan=15">83242</offset>
2734 <offset idRef="controllerType=0 controllerNumber=1 scan=16">87497</offset> 2737 <offset idRef="controllerType=0 controllerNumber=1 scan=16">87618</offset>
2735 <offset idRef="controllerType=0 controllerNumber=1 scan=17">91882</offset> 2738 <offset idRef="controllerType=0 controllerNumber=1 scan=17">92003</offset>
2736 <offset idRef="controllerType=0 controllerNumber=1 scan=18">97914</offset> 2739 <offset idRef="controllerType=0 controllerNumber=1 scan=18">98035</offset>
2737 <offset idRef="controllerType=0 controllerNumber=1 scan=19">103937</offset> 2740 <offset idRef="controllerType=0 controllerNumber=1 scan=19">104058</offset>
2738 <offset idRef="controllerType=0 controllerNumber=1 scan=20">109916</offset> 2741 <offset idRef="controllerType=0 controllerNumber=1 scan=20">110037</offset>
2739 <offset idRef="controllerType=0 controllerNumber=1 scan=21">115913</offset> 2742 <offset idRef="controllerType=0 controllerNumber=1 scan=21">116034</offset>
2740 <offset idRef="controllerType=0 controllerNumber=1 scan=22">121912</offset> 2743 <offset idRef="controllerType=0 controllerNumber=1 scan=22">122033</offset>
2741 <offset idRef="controllerType=0 controllerNumber=1 scan=23">126285</offset> 2744 <offset idRef="controllerType=0 controllerNumber=1 scan=23">126406</offset>
2742 <offset idRef="controllerType=0 controllerNumber=1 scan=24">130623</offset> 2745 <offset idRef="controllerType=0 controllerNumber=1 scan=24">130744</offset>
2743 <offset idRef="controllerType=0 controllerNumber=1 scan=25">136653</offset> 2746 <offset idRef="controllerType=0 controllerNumber=1 scan=25">136774</offset>
2744 <offset idRef="controllerType=0 controllerNumber=1 scan=26">142682</offset> 2747 <offset idRef="controllerType=0 controllerNumber=1 scan=26">142803</offset>
2745 <offset idRef="controllerType=0 controllerNumber=1 scan=27">148660</offset> 2748 <offset idRef="controllerType=0 controllerNumber=1 scan=27">148781</offset>
2746 <offset idRef="controllerType=0 controllerNumber=1 scan=28">154651</offset> 2749 <offset idRef="controllerType=0 controllerNumber=1 scan=28">154772</offset>
2747 <offset idRef="controllerType=0 controllerNumber=1 scan=29">160666</offset> 2750 <offset idRef="controllerType=0 controllerNumber=1 scan=29">160787</offset>
2748 <offset idRef="controllerType=0 controllerNumber=1 scan=30">165037</offset> 2751 <offset idRef="controllerType=0 controllerNumber=1 scan=30">165158</offset>
2749 <offset idRef="controllerType=0 controllerNumber=1 scan=31">169437</offset> 2752 <offset idRef="controllerType=0 controllerNumber=1 scan=31">169558</offset>
2750 <offset idRef="controllerType=0 controllerNumber=1 scan=32">175462</offset> 2753 <offset idRef="controllerType=0 controllerNumber=1 scan=32">175583</offset>
2751 <offset idRef="controllerType=0 controllerNumber=1 scan=33">181434</offset> 2754 <offset idRef="controllerType=0 controllerNumber=1 scan=33">181555</offset>
2752 <offset idRef="controllerType=0 controllerNumber=1 scan=34">187419</offset> 2755 <offset idRef="controllerType=0 controllerNumber=1 scan=34">187540</offset>
2753 <offset idRef="controllerType=0 controllerNumber=1 scan=35">193365</offset> 2756 <offset idRef="controllerType=0 controllerNumber=1 scan=35">193486</offset>
2754 <offset idRef="controllerType=0 controllerNumber=1 scan=36">197742</offset> 2757 <offset idRef="controllerType=0 controllerNumber=1 scan=36">197863</offset>
2755 <offset idRef="controllerType=0 controllerNumber=1 scan=37">202117</offset> 2758 <offset idRef="controllerType=0 controllerNumber=1 scan=37">202238</offset>
2756 <offset idRef="controllerType=0 controllerNumber=1 scan=38">208147</offset> 2759 <offset idRef="controllerType=0 controllerNumber=1 scan=38">208268</offset>
2757 <offset idRef="controllerType=0 controllerNumber=1 scan=39">214180</offset> 2760 <offset idRef="controllerType=0 controllerNumber=1 scan=39">214301</offset>
2758 <offset idRef="controllerType=0 controllerNumber=1 scan=40">220165</offset> 2761 <offset idRef="controllerType=0 controllerNumber=1 scan=40">220286</offset>
2759 <offset idRef="controllerType=0 controllerNumber=1 scan=41">226168</offset> 2762 <offset idRef="controllerType=0 controllerNumber=1 scan=41">226289</offset>
2760 <offset idRef="controllerType=0 controllerNumber=1 scan=42">232145</offset> 2763 <offset idRef="controllerType=0 controllerNumber=1 scan=42">232266</offset>
2761 <offset idRef="controllerType=0 controllerNumber=1 scan=43">236509</offset> 2764 <offset idRef="controllerType=0 controllerNumber=1 scan=43">236630</offset>
2762 <offset idRef="controllerType=0 controllerNumber=1 scan=44">240905</offset> 2765 <offset idRef="controllerType=0 controllerNumber=1 scan=44">241026</offset>
2763 <offset idRef="controllerType=0 controllerNumber=1 scan=45">246931</offset> 2766 <offset idRef="controllerType=0 controllerNumber=1 scan=45">247052</offset>
2764 <offset idRef="controllerType=0 controllerNumber=1 scan=46">252947</offset> 2767 <offset idRef="controllerType=0 controllerNumber=1 scan=46">253068</offset>
2765 <offset idRef="controllerType=0 controllerNumber=1 scan=47">258915</offset> 2768 <offset idRef="controllerType=0 controllerNumber=1 scan=47">259036</offset>
2766 <offset idRef="controllerType=0 controllerNumber=1 scan=48">264893</offset> 2769 <offset idRef="controllerType=0 controllerNumber=1 scan=48">265014</offset>
2767 </index> 2770 </index>
2768 <index name="chromatogram"> 2771 <index name="chromatogram">
2769 <offset idRef="TIC">270956</offset> 2772 <offset idRef="TIC">271077</offset>
2770 </index> 2773 </index>
2771 </indexList> 2774 </indexList>
2772 <indexListOffset>272906</indexListOffset> 2775 <indexListOffset>273027</indexListOffset>
2773 <fileChecksum>03196871e50429543745f1b16df164a19bced1f6</fileChecksum> 2776 <fileChecksum>b1908e0016bbf6bf4fc21daa511924db77237312</fileChecksum>
2774 </indexedmzML> 2777 </indexedmzML>