Mercurial > repos > galaxyp > cardinal_classification

comparison test-data/12_combined.imzml @ 5:42f6e30b00f2 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/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
author galaxyp
date Fri, 13 Dec 2019 13:55:06 -0500
parents
children 6f4c34f8d5ba
comparison
equal deleted inserted replaced
4:47fc5b518ffc 5:42f6e30b00f2
1 <?xml version="1.0"?>
2 <mzML version="1.1" 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_idx.xsd">
3 <cvList count="3">
4 <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />
5 <cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/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" value="" />
11 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
12 <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="e9aca5c3-32c8-416b-a9e9-e40ba239ce32" />
13 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c0c53177dc3a008c7a18ba10fe139ccaecc295a2" />
14 <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
15 </fileContent>
16 </fileDescription>
17 <referenceableParamGroupList count="4">
18 <referenceableParamGroup id="spectrum1">
19 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
20 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />
21 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
22 </referenceableParamGroup>
23 <referenceableParamGroup id="scan1">
24 <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
25 </referenceableParamGroup>
26 <referenceableParamGroup id="mzArray">
27 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
28 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
29 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
30 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
31 </referenceableParamGroup>
32 <referenceableParamGroup id="intensityArray">
33 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
34 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
35 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
36 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
37 </referenceableParamGroup>
38 </referenceableParamGroupList>
39 <sampleList count="1">
40 <sample id="sample1" name="Sample1">
41 <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />
42 </sample>
43 </sampleList>
44 <softwareList count="1">
45 <software id="Cardinal" version="2.2.6">
46 <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
47 </software>
48 </softwareList>
49 <scanSettingsList count="1">
50 <scanSettings id="scansettings1">
51 <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
52 <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
53 <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="8" />
54 <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />
55 <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />
56 <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />
57 </scanSettings>
58 </scanSettingsList>
59 <instrumentConfigurationList count="1">
60 <instrumentConfiguration id="IC1">
61 <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
62 </instrumentConfiguration>
63 </instrumentConfigurationList>
64 <dataProcessingList count="1">
65 <dataProcessing id="CardinalWriteImzML">
66 <processingMethod order="1" softwareRef="Cardinal">
67 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />
68 </processingMethod>
69 </dataProcessing>
70 </dataProcessingList>
71 <run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">
72 <spectrumList count="9" defaultDataProcessingRef="CardinalWriteImzML">
73 <spectrum id="Spectrum=1" defaultArrayLength="0" index="1">
74 <referenceableParamGroupRef ref="spectrum1" />
75 <scanList count="1">
76 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
77 <scan instrumentConfigurationRef="IC1">
78 <referenceableParamGroupRef ref="scan1" />
79 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
80 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
81 </scan>
82 </scanList>
83 <binaryDataArrayList count="2">
84 <binaryDataArray encodedLength="0">
85 <referenceableParamGroupRef ref="mzArray" />
86 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
87 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
88 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
89 <binary />
90 </binaryDataArray>
91 <binaryDataArray encodedLength="0">
92 <referenceableParamGroupRef ref="intensityArray" />
93 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33612" />
94 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
95 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
96 <binary />
97 </binaryDataArray>
98 </binaryDataArrayList>
99 </spectrum>
100 <spectrum id="Spectrum=2" defaultArrayLength="0" index="2">
101 <referenceableParamGroupRef ref="spectrum1" />
102 <scanList count="1">
103 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
104 <scan instrumentConfigurationRef="IC1">
105 <referenceableParamGroupRef ref="scan1" />
106 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
107 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
108 </scan>
109 </scanList>
110 <binaryDataArrayList count="2">
111 <binaryDataArray encodedLength="0">
112 <referenceableParamGroupRef ref="mzArray" />
113 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
114 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
115 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
116 <binary />
117 </binaryDataArray>
118 <binaryDataArray encodedLength="0">
119 <referenceableParamGroupRef ref="intensityArray" />
120 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208" />
121 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
122 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
123 <binary />
124 </binaryDataArray>
125 </binaryDataArrayList>
126 </spectrum>
127 <spectrum id="Spectrum=3" defaultArrayLength="0" index="3">
128 <referenceableParamGroupRef ref="spectrum1" />
129 <scanList count="1">
130 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
131 <scan instrumentConfigurationRef="IC1">
132 <referenceableParamGroupRef ref="scan1" />
133 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
134 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
135 </scan>
136 </scanList>
137 <binaryDataArrayList count="2">
138 <binaryDataArray encodedLength="0">
139 <referenceableParamGroupRef ref="mzArray" />
140 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
141 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
142 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
143 <binary />
144 </binaryDataArray>
145 <binaryDataArray encodedLength="0">
146 <referenceableParamGroupRef ref="intensityArray" />
147 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100804" />
148 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
149 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
150 <binary />
151 </binaryDataArray>
152 </binaryDataArrayList>
153 </spectrum>
154 <spectrum id="Spectrum=4" defaultArrayLength="0" index="4">
155 <referenceableParamGroupRef ref="spectrum1" />
156 <scanList count="1">
157 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
158 <scan instrumentConfigurationRef="IC1">
159 <referenceableParamGroupRef ref="scan1" />
160 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
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="8399" />
169 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
170 <binary />
171 </binaryDataArray>
172 <binaryDataArray encodedLength="0">
173 <referenceableParamGroupRef ref="intensityArray" />
174 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400" />
175 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
176 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
177 <binary />
178 </binaryDataArray>
179 </binaryDataArrayList>
180 </spectrum>
181 <spectrum id="Spectrum=5" defaultArrayLength="0" index="5">
182 <referenceableParamGroupRef ref="spectrum1" />
183 <scanList count="1">
184 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
185 <scan instrumentConfigurationRef="IC1">
186 <referenceableParamGroupRef ref="scan1" />
187 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="8" />
188 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
189 </scan>
190 </scanList>
191 <binaryDataArrayList count="2">
192 <binaryDataArray encodedLength="0">
193 <referenceableParamGroupRef ref="mzArray" />
194 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
195 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
196 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
197 <binary />
198 </binaryDataArray>
199 <binaryDataArray encodedLength="0">
200 <referenceableParamGroupRef ref="intensityArray" />
201 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996" />
202 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
203 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
204 <binary />
205 </binaryDataArray>
206 </binaryDataArrayList>
207 </spectrum>
208 <spectrum id="Spectrum=6" defaultArrayLength="0" index="6">
209 <referenceableParamGroupRef ref="spectrum1" />
210 <scanList count="1">
211 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
212 <scan instrumentConfigurationRef="IC1">
213 <referenceableParamGroupRef ref="scan1" />
214 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
215 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
216 </scan>
217 </scanList>
218 <binaryDataArrayList count="2">
219 <binaryDataArray encodedLength="0">
220 <referenceableParamGroupRef ref="mzArray" />
221 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
222 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
223 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
224 <binary />
225 </binaryDataArray>
226 <binaryDataArray encodedLength="0">
227 <referenceableParamGroupRef ref="intensityArray" />
228 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592" />
229 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
230 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
231 <binary />
232 </binaryDataArray>
233 </binaryDataArrayList>
234 </spectrum>
235 <spectrum id="Spectrum=7" defaultArrayLength="0" index="7">
236 <referenceableParamGroupRef ref="spectrum1" />
237 <scanList count="1">
238 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
239 <scan instrumentConfigurationRef="IC1">
240 <referenceableParamGroupRef ref="scan1" />
241 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="8" />
242 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
243 </scan>
244 </scanList>
245 <binaryDataArrayList count="2">
246 <binaryDataArray encodedLength="0">
247 <referenceableParamGroupRef ref="mzArray" />
248 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
249 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
250 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
251 <binary />
252 </binaryDataArray>
253 <binaryDataArray encodedLength="0">
254 <referenceableParamGroupRef ref="intensityArray" />
255 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188" />
256 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
257 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
258 <binary />
259 </binaryDataArray>
260 </binaryDataArrayList>
261 </spectrum>
262 <spectrum id="Spectrum=8" defaultArrayLength="0" index="8">
263 <referenceableParamGroupRef ref="spectrum1" />
264 <scanList count="1">
265 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
266 <scan instrumentConfigurationRef="IC1">
267 <referenceableParamGroupRef ref="scan1" />
268 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
269 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
270 </scan>
271 </scanList>
272 <binaryDataArrayList count="2">
273 <binaryDataArray encodedLength="0">
274 <referenceableParamGroupRef ref="mzArray" />
275 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
276 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
277 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
278 <binary />
279 </binaryDataArray>
280 <binaryDataArray encodedLength="0">
281 <referenceableParamGroupRef ref="intensityArray" />
282 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="268784" />
283 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
284 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
285 <binary />
286 </binaryDataArray>
287 </binaryDataArrayList>
288 </spectrum>
289 <spectrum id="Spectrum=9" defaultArrayLength="0" index="9">
290 <referenceableParamGroupRef ref="spectrum1" />
291 <scanList count="1">
292 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
293 <scan instrumentConfigurationRef="IC1">
294 <referenceableParamGroupRef ref="scan1" />
295 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="8" />
296 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
297 </scan>
298 </scanList>
299 <binaryDataArrayList count="2">
300 <binaryDataArray encodedLength="0">
301 <referenceableParamGroupRef ref="mzArray" />
302 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
303 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
304 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
305 <binary />
306 </binaryDataArray>
307 <binaryDataArray encodedLength="0">
308 <referenceableParamGroupRef ref="intensityArray" />
309 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380" />
310 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
311 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
312 <binary />
313 </binaryDataArray>
314 </binaryDataArrayList>
315 </spectrum>
316 </spectrumList>
317 </run>
318 </mzML>