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comparison test-data/BrukerBafTest.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
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children 6153e8ada1ee
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9:dd4ba10d0c45 10:9d5de24e6ef7
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">
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="BrukerBafTest" version="1.1.0">
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"/>
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>
8 <fileDescription>
9 <fileContent>
10 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
11 </fileContent>
12 <sourceFileList count="1">
13 <sourceFile id="BrukerBafTest.d_x005c_Analysis.baf" name="Analysis.baf" location="file:///">
14 <cvParam cvRef="MS" accession="MS:1000772" name="Bruker BAF nativeID format" value=""/>
15 <cvParam cvRef="MS" accession="MS:1000815" name="Bruker BAF format" value=""/>
16 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="5e1b8f06983c2e671a4a96714721c327f1e67ee1"/>
17 </sourceFile>
18 </sourceFileList>
19 </fileDescription>
20 <referenceableParamGroupList count="1">
21 <referenceableParamGroup id="CommonInstrumentParams">
22 <cvParam cvRef="MS" accession="MS:1001556" name="Bruker Daltonics apex series" value=""/>
23 </referenceableParamGroup>
24 </referenceableParamGroupList>
25 <softwareList count="3">
26 <software id="BAF2SQL" version="2.7.300.20-112">
27 <cvParam cvRef="MS" accession="MS:1000692" name="Bruker software" value=""/>
28 <userParam name="software name" value="BAF2SQL"/>
29 </software>
30 <software id="apexControl" version="ApexControl 3.0.0.alpha.35 (development version, April 18, 2008)">
31 <cvParam cvRef="MS" accession="MS:1000706" name="apexControl" value=""/>
32 </software>
33 <software id="pwiz_Reader_Bruker" version="3.0.19044">
34 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
35 </software>
36 </softwareList>
37 <instrumentConfigurationList count="1">
38 <instrumentConfiguration id="IC1">
39 <referenceableParamGroupRef ref="CommonInstrumentParams"/>
40 <componentList count="3">
41 <source order="1">
42 <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
43 <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/>
44 </source>
45 <analyzer order="2">
46 <cvParam cvRef="MS" accession="MS:1000079" name="fourier transform ion cyclotron resonance mass spectrometer" value=""/>
47 </analyzer>
48 <detector order="3">
49 <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>
50 </detector>
51 </componentList>
52 <softwareRef ref="apexControl"/>
53 </instrumentConfiguration>
54 </instrumentConfigurationList>
55 <dataProcessingList count="1">
56 <dataProcessing id="pwiz_Reader_Bruker_conversion">
57 <processingMethod order="0" softwareRef="pwiz_Reader_Bruker">
58 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
59 </processingMethod>
60 <processingMethod order="1" softwareRef="pwiz_Reader_Bruker">
61 <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
62 <userParam name="Bruker/Agilent/CompassXtract peak picking"/>
63 </processingMethod>
64 </dataProcessing>
65 </dataProcessingList>
66 <run id="BrukerBafTest" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2008-11-04T10:55:29Z" defaultSourceFileRef="BrukerBafTest.d_x005c_Analysis.baf">
67 <spectrumList count="1" defaultDataProcessingRef="pwiz_Reader_Bruker_conversion">
68 <spectrum index="0" id="scan=1" defaultArrayLength="71">
69 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
70 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
71 <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
72 <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="7.81485056e08"/>
73 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="5.704013312e09"/>
74 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
75 <scanList count="1">
76 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
77 <scan>
78 <scanWindowList count="1">
79 <scanWindow>
80 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="347.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
81 <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
82 </scanWindow>
83 </scanWindowList>
84 </scan>
85 </scanList>
86 <binaryDataArrayList count="2">
87 <binaryDataArray encodedLength="744">
88 <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
89 <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
90 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
91 <binary>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</binary>
92 </binaryDataArray>
93 <binaryDataArray encodedLength="396">
94 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
95 <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
96 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
97 <binary>eJwBHAHj/rDDDUyYqRlNHLfVSxCnz0tc0wNLIDP1SmBcI0wQODFMYEmGTYgzNkswU3FNYM99S4DvDEuAMXBNgDszTPB3ik3gYWBMcEOoS2DxQ0sgjjlLgEhLS6D3jUug3GJNUHMlToAmSkwAz7RLAKpPSwBFDkuAY2dLIGWbTID6CU0AvElLAB7zSmCQKkuAQKVLQIj0S+Bbk0wQUjpO4L3LS6C+kEvAXiNLwKgTS8DUMkxg5m5MoNNNTaD2gE3gcihLIA9ES2C5iUuAQARLQIwES4BHNEuA7qdLwMYuS4AHeEvAxgtLwKW6S8BuokvAQVpMQC09TEAwnUvAXlNNAHxfSyALAE2AYt5LgAduS8Ayvk2Ao1hLwAIsSwDi9EqAPGFLsyVy9w==</binary>
98 </binaryDataArray>
99 </binaryDataArrayList>
100 </spectrum>
101 </spectrumList>
102 </run>
103 </mzML>
104 <indexList count="2">
105 <index name="spectrum">
106 <offset idRef="scan=1">4166</offset>
107 </index>
108 <index name="chromatogram">
109 </index>
110 </indexList>
111 <indexListOffset>7590</indexListOffset>
112 <fileChecksum>e6b4d51fdbe306f0823fe1cb583e7ec52629303f</fileChecksum>
113 </indexedmzML>