Mercurial > repos > galaxyp > cardinal_segmentations

comparison test-data/ComBat_results_Example_processed_file.imzml @ 16:df2187f9013b 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 eeeb69463a2037a6ee620b9223cb152fcc39f1b0
author galaxyp
date Wed, 19 Apr 2023 22:47:48 +0000
parents
children 91f0f5922011
comparison
equal deleted inserted replaced
15:653ad2b367f2 16:df2187f9013b
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="82e7db90-df72-41f8-9ca7-7a19e966d5c1" />
13 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="259aa4b90129abb2f1f3107cf123f28d7c744f0c" />
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="2.10.0">
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:1000401" name="top down" value="" />
52 <cvParam cvRef="IMS" accession="IMS:1000413" name="flyback" value="" />
53 <cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan" value="" />
54 <cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right" value="" />
55 <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
56 <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
57 <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />
58 <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />
59 <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />
60 <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />
61 </scanSettings>
62 </scanSettingsList>
63 <instrumentConfigurationList count="1">
64 <instrumentConfiguration id="IC1">
65 <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
66 </instrumentConfiguration>
67 </instrumentConfigurationList>
68 <dataProcessingList count="1">
69 <dataProcessing id="CardinalWriteImzML">
70 <processingMethod order="1" softwareRef="Cardinal">
71 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />
72 </processingMethod>
73 </dataProcessing>
74 </dataProcessingList>
75 <run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">
76 <spectrumList count="9" defaultDataProcessingRef="CardinalWriteImzML">
77 <spectrum id="Spectrum=1" defaultArrayLength="0" index="1">
78 <referenceableParamGroupRef ref="spectrum1" />
79 <scanList count="1">
80 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
81 <scan instrumentConfigurationRef="IC1">
82 <referenceableParamGroupRef ref="scan1" />
83 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
84 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
85 <userParam name="3DPositionX" value="1.000000" />
86 <userParam name="3DPositionY" value="1.000000" />
87 </scan>
88 </scanList>
89 <binaryDataArrayList count="2">
90 <binaryDataArray encodedLength="0">
91 <referenceableParamGroupRef ref="mzArray" />
92 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
93 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
94 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
95 <binary />
96 </binaryDataArray>
97 <binaryDataArray encodedLength="0">
98 <referenceableParamGroupRef ref="intensityArray" />
99 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="166372" />
100 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
101 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
102 <binary />
103 </binaryDataArray>
104 </binaryDataArrayList>
105 </spectrum>
106 <spectrum id="Spectrum=2" defaultArrayLength="0" index="2">
107 <referenceableParamGroupRef ref="spectrum1" />
108 <scanList count="1">
109 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
110 <scan instrumentConfigurationRef="IC1">
111 <referenceableParamGroupRef ref="scan1" />
112 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
113 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
114 <userParam name="3DPositionX" value="2.000000" />
115 <userParam name="3DPositionY" value="1.000000" />
116 </scan>
117 </scanList>
118 <binaryDataArrayList count="2">
119 <binaryDataArray encodedLength="0">
120 <referenceableParamGroupRef ref="mzArray" />
121 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
122 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
123 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
124 <binary />
125 </binaryDataArray>
126 <binaryDataArray encodedLength="0">
127 <referenceableParamGroupRef ref="intensityArray" />
128 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="332728" />
129 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
130 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
131 <binary />
132 </binaryDataArray>
133 </binaryDataArrayList>
134 </spectrum>
135 <spectrum id="Spectrum=3" defaultArrayLength="0" index="3">
136 <referenceableParamGroupRef ref="spectrum1" />
137 <scanList count="1">
138 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
139 <scan instrumentConfigurationRef="IC1">
140 <referenceableParamGroupRef ref="scan1" />
141 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
142 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
143 <userParam name="3DPositionX" value="3.000000" />
144 <userParam name="3DPositionY" value="1.000000" />
145 </scan>
146 </scanList>
147 <binaryDataArrayList count="2">
148 <binaryDataArray encodedLength="0">
149 <referenceableParamGroupRef ref="mzArray" />
150 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
151 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
152 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
153 <binary />
154 </binaryDataArray>
155 <binaryDataArray encodedLength="0">
156 <referenceableParamGroupRef ref="intensityArray" />
157 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="499084" />
158 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
159 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
160 <binary />
161 </binaryDataArray>
162 </binaryDataArrayList>
163 </spectrum>
164 <spectrum id="Spectrum=4" defaultArrayLength="0" index="4">
165 <referenceableParamGroupRef ref="spectrum1" />
166 <scanList count="1">
167 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
168 <scan instrumentConfigurationRef="IC1">
169 <referenceableParamGroupRef ref="scan1" />
170 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
171 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
172 <userParam name="3DPositionX" value="1.000000" />
173 <userParam name="3DPositionY" value="2.000000" />
174 </scan>
175 </scanList>
176 <binaryDataArrayList count="2">
177 <binaryDataArray encodedLength="0">
178 <referenceableParamGroupRef ref="mzArray" />
179 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
180 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
181 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
182 <binary />
183 </binaryDataArray>
184 <binaryDataArray encodedLength="0">
185 <referenceableParamGroupRef ref="intensityArray" />
186 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="665440" />
187 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
188 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
189 <binary />
190 </binaryDataArray>
191 </binaryDataArrayList>
192 </spectrum>
193 <spectrum id="Spectrum=5" defaultArrayLength="0" index="5">
194 <referenceableParamGroupRef ref="spectrum1" />
195 <scanList count="1">
196 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
197 <scan instrumentConfigurationRef="IC1">
198 <referenceableParamGroupRef ref="scan1" />
199 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
200 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
201 <userParam name="3DPositionX" value="2.000000" />
202 <userParam name="3DPositionY" value="2.000000" />
203 </scan>
204 </scanList>
205 <binaryDataArrayList count="2">
206 <binaryDataArray encodedLength="0">
207 <referenceableParamGroupRef ref="mzArray" />
208 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
209 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
210 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
211 <binary />
212 </binaryDataArray>
213 <binaryDataArray encodedLength="0">
214 <referenceableParamGroupRef ref="intensityArray" />
215 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="831796" />
216 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
217 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
218 <binary />
219 </binaryDataArray>
220 </binaryDataArrayList>
221 </spectrum>
222 <spectrum id="Spectrum=6" defaultArrayLength="0" index="6">
223 <referenceableParamGroupRef ref="spectrum1" />
224 <scanList count="1">
225 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
226 <scan instrumentConfigurationRef="IC1">
227 <referenceableParamGroupRef ref="scan1" />
228 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
229 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
230 <userParam name="3DPositionX" value="3.000000" />
231 <userParam name="3DPositionY" value="2.000000" />
232 </scan>
233 </scanList>
234 <binaryDataArrayList count="2">
235 <binaryDataArray encodedLength="0">
236 <referenceableParamGroupRef ref="mzArray" />
237 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
238 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
239 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
240 <binary />
241 </binaryDataArray>
242 <binaryDataArray encodedLength="0">
243 <referenceableParamGroupRef ref="intensityArray" />
244 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="998152" />
245 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
246 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
247 <binary />
248 </binaryDataArray>
249 </binaryDataArrayList>
250 </spectrum>
251 <spectrum id="Spectrum=7" defaultArrayLength="0" index="7">
252 <referenceableParamGroupRef ref="spectrum1" />
253 <scanList count="1">
254 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
255 <scan instrumentConfigurationRef="IC1">
256 <referenceableParamGroupRef ref="scan1" />
257 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
258 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
259 <userParam name="3DPositionX" value="1.000000" />
260 <userParam name="3DPositionY" value="3.000000" />
261 </scan>
262 </scanList>
263 <binaryDataArrayList count="2">
264 <binaryDataArray encodedLength="0">
265 <referenceableParamGroupRef ref="mzArray" />
266 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
267 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
268 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
269 <binary />
270 </binaryDataArray>
271 <binaryDataArray encodedLength="0">
272 <referenceableParamGroupRef ref="intensityArray" />
273 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1164508" />
274 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
275 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
276 <binary />
277 </binaryDataArray>
278 </binaryDataArrayList>
279 </spectrum>
280 <spectrum id="Spectrum=8" defaultArrayLength="0" index="8">
281 <referenceableParamGroupRef ref="spectrum1" />
282 <scanList count="1">
283 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
284 <scan instrumentConfigurationRef="IC1">
285 <referenceableParamGroupRef ref="scan1" />
286 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
287 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
288 <userParam name="3DPositionX" value="2.000000" />
289 <userParam name="3DPositionY" value="3.000000" />
290 </scan>
291 </scanList>
292 <binaryDataArrayList count="2">
293 <binaryDataArray encodedLength="0">
294 <referenceableParamGroupRef ref="mzArray" />
295 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
296 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
297 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
298 <binary />
299 </binaryDataArray>
300 <binaryDataArray encodedLength="0">
301 <referenceableParamGroupRef ref="intensityArray" />
302 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1330864" />
303 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
304 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
305 <binary />
306 </binaryDataArray>
307 </binaryDataArrayList>
308 </spectrum>
309 <spectrum id="Spectrum=9" defaultArrayLength="0" index="9">
310 <referenceableParamGroupRef ref="spectrum1" />
311 <scanList count="1">
312 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
313 <scan instrumentConfigurationRef="IC1">
314 <referenceableParamGroupRef ref="scan1" />
315 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
316 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
317 <userParam name="3DPositionX" value="3.000000" />
318 <userParam name="3DPositionY" value="3.000000" />
319 </scan>
320 </scanList>
321 <binaryDataArrayList count="2">
322 <binaryDataArray encodedLength="0">
323 <referenceableParamGroupRef ref="mzArray" />
324 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
325 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
326 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
327 <binary />
328 </binaryDataArray>
329 <binaryDataArray encodedLength="0">
330 <referenceableParamGroupRef ref="intensityArray" />
331 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1497220" />
332 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="41589" />
333 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="166356" />
334 <binary />
335 </binaryDataArray>
336 </binaryDataArrayList>
337 </spectrum>
338 </spectrumList>
339 </run>
340 </mzML>