Mercurial > repos > galaxyp > maldi_quant_peak_detection

comparison test-data/outfile1.imzml @ 3:36d38d2cf88c 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/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="{97729696-da30-4a3d-82ca-7f29db94e86d}"/>
12 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c4e5c9a9a6557c53ec74a6d728093019ab2bbc41"/>
13 <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous"/>
14 <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/>
15 </fileContent>
16 <sourceFileList count="1">
17 <sourceFile id="SF1" location="/tmp/tmp08K9FY/job_working_directory/000/3/working" name="infile.imzML">
18 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="0d2ad51f69d7b5df0f4d2b2a47b17478f2fca509"/>
19 </sourceFile>
20 </sourceFileList>
21 </fileDescription>
22 <softwareList count="1">
23 <software id="MALDIquantForeign" version="0.11.5"/>
24 </softwareList>
25 <referenceableParamGroupList count="2">
26 <referenceableParamGroup id="mzArray">
27 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
28 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
29 <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
30 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
31 </referenceableParamGroup>
32 <referenceableParamGroup id="intensityArray">
33 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
34 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
35 <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
36 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
37 </referenceableParamGroup>
38 </referenceableParamGroupList>
39 <scanSettingsList count="1">
40 <scanSettings id="scansetting1">
41 <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3"/>
42 <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3"/>
43 <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
44 <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
45 <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
46 <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
47 </scanSettings>
48 </scanSettingsList>
49 <instrumentConfigurationList count="1">
50 <instrumentConfiguration id="IC0"/>
51 </instrumentConfigurationList>
52 <dataProcessingList count="1">
53 <dataProcessing id="export">
54 <processingMethod order="1" softwareRef="MALDIquantForeign">
55 <userParam name="MALDIquant object(s) exported to mzML" value=""/>
56 </processingMethod>
57 </dataProcessing>
58 </dataProcessingList>
59 <run id="run0" defaultInstrumentConfigurationRef="IC0">
60 <spectrumList count="6" defaultDataProcessingRef="export">
61 <spectrum index="0" id="Spectrum=1" defaultArrayLength="1199">
62 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
63 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
64 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="300.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
65 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="399.916687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
66 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
67 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="2.44841884215683"/>
68 <scanList count="1">
69 <scan>
70 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
71 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
72 </scan>
73 </scanList>
74 <binaryDataArrayList count="2">
75 <binaryDataArray encodedLength="0">
76 <referenceableParamGroupRef ref="mzArray"/>
77 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
78 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
79 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
80 <binary/>
81 </binaryDataArray>
82 <binaryDataArray encodedLength="0">
83 <referenceableParamGroupRef ref="intensityArray"/>
84 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="9608"/>
85 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
86 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
87 <binary/>
88 </binaryDataArray>
89 </binaryDataArrayList>
90 </spectrum>
91 <spectrum index="1" id="Spectrum=4" defaultArrayLength="1199">
92 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
93 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
94 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="300.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
95 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="399.916687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
96 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
97 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="4.72366236736229"/>
98 <scanList count="1">
99 <scan>
100 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
101 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
102 </scan>
103 </scanList>
104 <binaryDataArrayList count="2">
105 <binaryDataArray encodedLength="0">
106 <referenceableParamGroupRef ref="mzArray"/>
107 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
108 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
109 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
110 <binary/>
111 </binaryDataArray>
112 <binaryDataArray encodedLength="0">
113 <referenceableParamGroupRef ref="intensityArray"/>
114 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="19200"/>
115 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
116 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
117 <binary/>
118 </binaryDataArray>
119 </binaryDataArrayList>
120 </spectrum>
121 <spectrum index="2" id="Spectrum=7" defaultArrayLength="1199">
122 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
123 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
124 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="300.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
125 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="399.916687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
126 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
127 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="2.34697718761883"/>
128 <scanList count="1">
129 <scan>
130 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
131 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
132 </scan>
133 </scanList>
134 <binaryDataArrayList count="2">
135 <binaryDataArray encodedLength="0">
136 <referenceableParamGroupRef ref="mzArray"/>
137 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
138 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
139 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
140 <binary/>
141 </binaryDataArray>
142 <binaryDataArray encodedLength="0">
143 <referenceableParamGroupRef ref="intensityArray"/>
144 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="28792"/>
145 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
146 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
147 <binary/>
148 </binaryDataArray>
149 </binaryDataArrayList>
150 </spectrum>
151 <spectrum index="3" id="Spectrum=3" defaultArrayLength="1199">
152 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
153 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
154 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="300.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
155 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="399.916687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
156 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
157 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="3.39025471907476"/>
158 <scanList count="1">
159 <scan>
160 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
161 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
162 </scan>
163 </scanList>
164 <binaryDataArrayList count="2">
165 <binaryDataArray encodedLength="0">
166 <referenceableParamGroupRef ref="mzArray"/>
167 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
168 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
169 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
170 <binary/>
171 </binaryDataArray>
172 <binaryDataArray encodedLength="0">
173 <referenceableParamGroupRef ref="intensityArray"/>
174 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="38384"/>
175 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
176 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
177 <binary/>
178 </binaryDataArray>
179 </binaryDataArrayList>
180 </spectrum>
181 <spectrum index="4" id="Spectrum=6" defaultArrayLength="1199">
182 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
183 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
184 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="300.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
185 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="399.916687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
186 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
187 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1.5591991257541"/>
188 <scanList count="1">
189 <scan>
190 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
191 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
192 </scan>
193 </scanList>
194 <binaryDataArrayList count="2">
195 <binaryDataArray encodedLength="0">
196 <referenceableParamGroupRef ref="mzArray"/>
197 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
198 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
199 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
200 <binary/>
201 </binaryDataArray>
202 <binaryDataArray encodedLength="0">
203 <referenceableParamGroupRef ref="intensityArray"/>
204 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="47976"/>
205 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
206 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
207 <binary/>
208 </binaryDataArray>
209 </binaryDataArrayList>
210 </spectrum>
211 <spectrum index="5" id="Spectrum=9" defaultArrayLength="1199">
212 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
213 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
214 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="300.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
215 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="399.916687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
216 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
217 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="4.31553230835188"/>
218 <scanList count="1">
219 <scan>
220 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
221 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
222 </scan>
223 </scanList>
224 <binaryDataArrayList count="2">
225 <binaryDataArray encodedLength="0">
226 <referenceableParamGroupRef ref="mzArray"/>
227 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
228 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
229 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
230 <binary/>
231 </binaryDataArray>
232 <binaryDataArray encodedLength="0">
233 <referenceableParamGroupRef ref="intensityArray"/>
234 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="57568"/>
235 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199"/>
236 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9592"/>
237 <binary/>
238 </binaryDataArray>
239 </binaryDataArrayList>
240 </spectrum>
241 </spectrumList>
242 </run>
243 </mzML>