comparison test-data/outfile2.imzml @ 3:36d38d2cf88c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
author galaxyp
date Fri, 15 Feb 2019 10:26:45 -0500
parents
children
comparison
equal deleted inserted replaced
2:17c54820f3be 3:36d38d2cf88c
1 <?xml version="1.0" encoding="utf-8"?>
2 <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="out" version="1.1.0">
3 <cvList count="2">
4 <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.44.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
5 <cv id="UO" fullName="Unit Ontology" version="12:10:2012" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
6 <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>
7 </cvList>
8 <fileDescription>
9 <fileContent>
10 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
11 <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{54a5519e-643b-4eb1-b82b-d55aaa5e9015}"/>
12 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="12d68eada8b274b1bba9520cef0ff98d6fc95bf4"/>
13 <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous"/>
14 <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/>
15 </fileContent>
16 </fileDescription>
17 <softwareList count="1">
18 <software id="MALDIquantForeign" version="0.11.5"/>
19 </softwareList>
20 <referenceableParamGroupList count="2">
21 <referenceableParamGroup id="mzArray">
22 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
23 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
24 <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
25 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
26 </referenceableParamGroup>
27 <referenceableParamGroup id="intensityArray">
28 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
29 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
30 <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
31 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
32 </referenceableParamGroup>
33 </referenceableParamGroupList>
34 <scanSettingsList count="1">
35 <scanSettings id="scansetting1">
36 <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="1"/>
37 <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3"/>
38 <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
39 <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
40 <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
41 <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
42 </scanSettings>
43 </scanSettingsList>
44 <instrumentConfigurationList count="1">
45 <instrumentConfiguration id="IC0"/>
46 </instrumentConfigurationList>
47 <dataProcessingList count="1">
48 <dataProcessing id="export">
49 <processingMethod order="1" softwareRef="MALDIquantForeign">
50 <userParam name="MALDIquant object(s) exported to mzML" value=""/>
51 </processingMethod>
52 </dataProcessing>
53 </dataProcessingList>
54 <run id="run0" defaultInstrumentConfigurationRef="IC0">
55 <spectrumList count="2" defaultDataProcessingRef="export">
56 <spectrum index="0" id="scan=0" defaultArrayLength="8399">
57 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
58 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
59 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="100.000007629395" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
60 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="799.816687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
61 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
62 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="16.7431673605698"/>
63 <scanList count="1">
64 <scan>
65 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
66 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
67 </scan>
68 </scanList>
69 <binaryDataArrayList count="2">
70 <binaryDataArray encodedLength="0">
71 <referenceableParamGroupRef ref="mzArray"/>
72 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
73 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
74 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
75 <binary/>
76 </binaryDataArray>
77 <binaryDataArray encodedLength="0">
78 <referenceableParamGroupRef ref="intensityArray"/>
79 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208"/>
80 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
81 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
82 <binary/>
83 </binaryDataArray>
84 </binaryDataArrayList>
85 </spectrum>
86 <spectrum index="1" id="scan=1" defaultArrayLength="8399">
87 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
88 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
89 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="100.083335876465" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
90 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="799.9" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
91 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
92 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="10.6534160746182"/>
93 <scanList count="1">
94 <scan>
95 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
96 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
97 </scan>
98 </scanList>
99 <binaryDataArrayList count="2">
100 <binaryDataArray encodedLength="0">
101 <referenceableParamGroupRef ref="mzArray"/>
102 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
103 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
104 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
105 <binary/>
106 </binaryDataArray>
107 <binaryDataArray encodedLength="0">
108 <referenceableParamGroupRef ref="intensityArray"/>
109 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400"/>
110 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
111 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
112 <binary/>
113 </binaryDataArray>
114 </binaryDataArrayList>
115 </spectrum>
116 </spectrumList>
117 </run>
118 </mzML>