Mercurial > repos > galaxyp > cardinal_preprocessing

comparison test-data/preprocessing_results1.imzml @ 2:1b875f0b8024 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 f127be2141cf22e269c85282d226eb16fe14a9c1
author galaxyp
date Fri, 15 Feb 2019 10:22:14 -0500
parents
children f172efe92629
comparison
equal deleted inserted replaced
1:1b22c1e7bfe7 2:1b875f0b8024
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:1000127" name="centroid spectrum" value="" />
12 <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{002DF5BA-0549-44DF-A8BB-27DA3E197EB7}" />
13 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0379019A6F9D0B55F9217420030633F7163AF9D3" />
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:1000127" name="centroid spectrum" value="" />
22 </referenceableParamGroup>
23 <referenceableParamGroup id="scan1">
24 <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
25 <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
26 </referenceableParamGroup>
27 <referenceableParamGroup id="mzArray">
28 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
29 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
30 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
31 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
32 </referenceableParamGroup>
33 <referenceableParamGroup id="intensityArray">
34 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
35 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
36 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
37 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
38 </referenceableParamGroup>
39 </referenceableParamGroupList>
40 <sampleList count="1">
41 <sample id="sample1" name="Sample1">
42 <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />
43 </sample>
44 </sampleList>
45 <softwareList count="1">
46 <software id="Cardinal" version="1.12.1">
47 <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
48 </software>
49 </softwareList>
50 <scanSettingsList count="1">
51 <scanSettings id="scansettings1">
52 <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
53 <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
54 </scanSettings>
55 </scanSettingsList>
56 <instrumentConfigurationList count="1">
57 <instrumentConfiguration id="IC1" />
58 </instrumentConfigurationList>
59 <dataProcessingList count="1">
60 <dataProcessing id="CardinalWriteImzML">
61 <processingMethod order="1" softwareRef="Cardinal">
62 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />
63 </processingMethod>
64 </dataProcessing>
65 </dataProcessingList>
66 <run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">
67 <spectrumList count="9" defaultDataProcessingRef="CardinalWriteImzML">
68 <spectrum id="Spectrum=1" defaultArrayLength="0" index="1">
69 <referenceableParamGroupRef ref="spectrum1" />
70 <scanList count="1">
71 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
72 <scan instrumentConfigurationRef="IC1">
73 <referenceableParamGroupRef ref="scan1" />
74 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
75 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
76 </scan>
77 </scanList>
78 <binaryDataArrayList count="2">
79 <binaryDataArray encodedLength="0">
80 <referenceableParamGroupRef ref="mzArray" />
81 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
82 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
83 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
84 <binary />
85 </binaryDataArray>
86 <binaryDataArray encodedLength="0">
87 <referenceableParamGroupRef ref="intensityArray" />
88 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="24" />
89 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
90 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
91 <binary />
92 </binaryDataArray>
93 </binaryDataArrayList>
94 </spectrum>
95 <spectrum id="Spectrum=2" defaultArrayLength="0" index="2">
96 <referenceableParamGroupRef ref="spectrum1" />
97 <scanList count="1">
98 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
99 <scan instrumentConfigurationRef="IC1">
100 <referenceableParamGroupRef ref="scan1" />
101 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
102 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
103 </scan>
104 </scanList>
105 <binaryDataArrayList count="2">
106 <binaryDataArray encodedLength="0">
107 <referenceableParamGroupRef ref="mzArray" />
108 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
109 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
110 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
111 <binary />
112 </binaryDataArray>
113 <binaryDataArray encodedLength="0">
114 <referenceableParamGroupRef ref="intensityArray" />
115 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="32" />
116 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
117 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
118 <binary />
119 </binaryDataArray>
120 </binaryDataArrayList>
121 </spectrum>
122 <spectrum id="Spectrum=3" defaultArrayLength="0" index="3">
123 <referenceableParamGroupRef ref="spectrum1" />
124 <scanList count="1">
125 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
126 <scan instrumentConfigurationRef="IC1">
127 <referenceableParamGroupRef ref="scan1" />
128 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
129 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
130 </scan>
131 </scanList>
132 <binaryDataArrayList count="2">
133 <binaryDataArray encodedLength="0">
134 <referenceableParamGroupRef ref="mzArray" />
135 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
136 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
137 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
138 <binary />
139 </binaryDataArray>
140 <binaryDataArray encodedLength="0">
141 <referenceableParamGroupRef ref="intensityArray" />
142 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="40" />
143 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
144 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
145 <binary />
146 </binaryDataArray>
147 </binaryDataArrayList>
148 </spectrum>
149 <spectrum id="Spectrum=4" defaultArrayLength="0" index="4">
150 <referenceableParamGroupRef ref="spectrum1" />
151 <scanList count="1">
152 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
153 <scan instrumentConfigurationRef="IC1">
154 <referenceableParamGroupRef ref="scan1" />
155 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
156 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
157 </scan>
158 </scanList>
159 <binaryDataArrayList count="2">
160 <binaryDataArray encodedLength="0">
161 <referenceableParamGroupRef ref="mzArray" />
162 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
163 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
164 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
165 <binary />
166 </binaryDataArray>
167 <binaryDataArray encodedLength="0">
168 <referenceableParamGroupRef ref="intensityArray" />
169 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="48" />
170 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
171 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
172 <binary />
173 </binaryDataArray>
174 </binaryDataArrayList>
175 </spectrum>
176 <spectrum id="Spectrum=5" defaultArrayLength="0" index="5">
177 <referenceableParamGroupRef ref="spectrum1" />
178 <scanList count="1">
179 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
180 <scan instrumentConfigurationRef="IC1">
181 <referenceableParamGroupRef ref="scan1" />
182 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
183 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
184 </scan>
185 </scanList>
186 <binaryDataArrayList count="2">
187 <binaryDataArray encodedLength="0">
188 <referenceableParamGroupRef ref="mzArray" />
189 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
190 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
191 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
192 <binary />
193 </binaryDataArray>
194 <binaryDataArray encodedLength="0">
195 <referenceableParamGroupRef ref="intensityArray" />
196 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="56" />
197 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
198 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
199 <binary />
200 </binaryDataArray>
201 </binaryDataArrayList>
202 </spectrum>
203 <spectrum id="Spectrum=6" defaultArrayLength="0" index="6">
204 <referenceableParamGroupRef ref="spectrum1" />
205 <scanList count="1">
206 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
207 <scan instrumentConfigurationRef="IC1">
208 <referenceableParamGroupRef ref="scan1" />
209 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
210 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
211 </scan>
212 </scanList>
213 <binaryDataArrayList count="2">
214 <binaryDataArray encodedLength="0">
215 <referenceableParamGroupRef ref="mzArray" />
216 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
217 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
218 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
219 <binary />
220 </binaryDataArray>
221 <binaryDataArray encodedLength="0">
222 <referenceableParamGroupRef ref="intensityArray" />
223 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="64" />
224 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
225 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
226 <binary />
227 </binaryDataArray>
228 </binaryDataArrayList>
229 </spectrum>
230 <spectrum id="Spectrum=7" defaultArrayLength="0" index="7">
231 <referenceableParamGroupRef ref="spectrum1" />
232 <scanList count="1">
233 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
234 <scan instrumentConfigurationRef="IC1">
235 <referenceableParamGroupRef ref="scan1" />
236 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
237 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
238 </scan>
239 </scanList>
240 <binaryDataArrayList count="2">
241 <binaryDataArray encodedLength="0">
242 <referenceableParamGroupRef ref="mzArray" />
243 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
244 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
245 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
246 <binary />
247 </binaryDataArray>
248 <binaryDataArray encodedLength="0">
249 <referenceableParamGroupRef ref="intensityArray" />
250 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="72" />
251 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
252 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
253 <binary />
254 </binaryDataArray>
255 </binaryDataArrayList>
256 </spectrum>
257 <spectrum id="Spectrum=8" defaultArrayLength="0" index="8">
258 <referenceableParamGroupRef ref="spectrum1" />
259 <scanList count="1">
260 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
261 <scan instrumentConfigurationRef="IC1">
262 <referenceableParamGroupRef ref="scan1" />
263 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
264 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
265 </scan>
266 </scanList>
267 <binaryDataArrayList count="2">
268 <binaryDataArray encodedLength="0">
269 <referenceableParamGroupRef ref="mzArray" />
270 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
271 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
272 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
273 <binary />
274 </binaryDataArray>
275 <binaryDataArray encodedLength="0">
276 <referenceableParamGroupRef ref="intensityArray" />
277 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="80" />
278 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
279 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
280 <binary />
281 </binaryDataArray>
282 </binaryDataArrayList>
283 </spectrum>
284 <spectrum id="Spectrum=9" defaultArrayLength="0" index="9">
285 <referenceableParamGroupRef ref="spectrum1" />
286 <scanList count="1">
287 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
288 <scan instrumentConfigurationRef="IC1">
289 <referenceableParamGroupRef ref="scan1" />
290 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
291 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
292 </scan>
293 </scanList>
294 <binaryDataArrayList count="2">
295 <binaryDataArray encodedLength="0">
296 <referenceableParamGroupRef ref="mzArray" />
297 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
298 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
299 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
300 <binary />
301 </binaryDataArray>
302 <binaryDataArray encodedLength="0">
303 <referenceableParamGroupRef ref="intensityArray" />
304 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="88" />
305 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
306 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
307 <binary />
308 </binaryDataArray>
309 </binaryDataArrayList>
310 </spectrum>
311 </spectrumList>
312 </run>
313 </mzML>