Mercurial > repos > galaxyp > maldi_quant_peak_detection

comparison test-data/peak_detection3.imzml @ 3:c42549f04fdd 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 10:14:01 -0500
parents
children 4bd085117204
comparison
equal deleted inserted replaced
2:41c148280a08 3:c42549f04fdd
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="{00515efe-60d8-4171-bb57-6f33c159ef7d}"/>
12 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="59e17ebe18b0559646ba7a17e709054397f086ea"/>
13 <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
14 <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/>
15 </fileContent>
16 <sourceFileList count="1">
17 <sourceFile id="SF1" location="/tmp/tmpPJKhfc/job_working_directory/000/8/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="9" defaultDataProcessingRef="export">
61 <spectrum index="0" id="Spectrum=1" defaultArrayLength="38">
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="304.595254080636" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
65 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
66 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
67 <scanList count="1">
68 <scan>
69 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
70 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
71 </scan>
72 </scanList>
73 <binaryDataArrayList count="2">
74 <binaryDataArray encodedLength="0">
75 <referenceableParamGroupRef ref="mzArray"/>
76 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
77 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
78 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
79 <binary/>
80 </binaryDataArray>
81 <binaryDataArray encodedLength="0">
82 <referenceableParamGroupRef ref="intensityArray"/>
83 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="320"/>
84 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
85 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
86 <binary/>
87 </binaryDataArray>
88 </binaryDataArrayList>
89 </spectrum>
90 <spectrum index="1" id="Spectrum=2" defaultArrayLength="33">
91 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
92 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
93 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="306.32292175293" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
94 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
95 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
96 <scanList count="1">
97 <scan>
98 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
99 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
100 </scan>
101 </scanList>
102 <binaryDataArrayList count="2">
103 <binaryDataArray encodedLength="0">
104 <referenceableParamGroupRef ref="mzArray"/>
105 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="624"/>
106 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
107 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
108 <binary/>
109 </binaryDataArray>
110 <binaryDataArray encodedLength="0">
111 <referenceableParamGroupRef ref="intensityArray"/>
112 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="888"/>
113 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
114 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
115 <binary/>
116 </binaryDataArray>
117 </binaryDataArrayList>
118 </spectrum>
119 <spectrum index="2" id="Spectrum=3" defaultArrayLength="28">
120 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
121 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
122 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="328.937515258789" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
123 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="396.916674804687" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
124 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
125 <scanList count="1">
126 <scan>
127 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
128 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
129 </scan>
130 </scanList>
131 <binaryDataArrayList count="2">
132 <binaryDataArray encodedLength="0">
133 <referenceableParamGroupRef ref="mzArray"/>
134 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1152"/>
135 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
136 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
137 <binary/>
138 </binaryDataArray>
139 <binaryDataArray encodedLength="0">
140 <referenceableParamGroupRef ref="intensityArray"/>
141 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1376"/>
142 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
143 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
144 <binary/>
145 </binaryDataArray>
146 </binaryDataArrayList>
147 </spectrum>
148 <spectrum index="3" id="Spectrum=4" defaultArrayLength="38">
149 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
150 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
151 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="304.595254080636" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
152 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
153 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
154 <scanList count="1">
155 <scan>
156 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
157 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
158 </scan>
159 </scanList>
160 <binaryDataArrayList count="2">
161 <binaryDataArray encodedLength="0">
162 <referenceableParamGroupRef ref="mzArray"/>
163 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1600"/>
164 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
165 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
166 <binary/>
167 </binaryDataArray>
168 <binaryDataArray encodedLength="0">
169 <referenceableParamGroupRef ref="intensityArray"/>
170 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1904"/>
171 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
172 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
173 <binary/>
174 </binaryDataArray>
175 </binaryDataArrayList>
176 </spectrum>
177 <spectrum index="4" id="Spectrum=5" defaultArrayLength="33">
178 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
179 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
180 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="306.32292175293" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
181 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
182 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
183 <scanList count="1">
184 <scan>
185 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
186 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
187 </scan>
188 </scanList>
189 <binaryDataArrayList count="2">
190 <binaryDataArray encodedLength="0">
191 <referenceableParamGroupRef ref="mzArray"/>
192 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="2208"/>
193 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
194 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
195 <binary/>
196 </binaryDataArray>
197 <binaryDataArray encodedLength="0">
198 <referenceableParamGroupRef ref="intensityArray"/>
199 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="2472"/>
200 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
201 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
202 <binary/>
203 </binaryDataArray>
204 </binaryDataArrayList>
205 </spectrum>
206 <spectrum index="5" id="Spectrum=6" defaultArrayLength="28">
207 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
208 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
209 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="328.937515258789" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
210 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="396.916674804687" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
211 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
212 <scanList count="1">
213 <scan>
214 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
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="2736"/>
222 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
223 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
224 <binary/>
225 </binaryDataArray>
226 <binaryDataArray encodedLength="0">
227 <referenceableParamGroupRef ref="intensityArray"/>
228 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="2960"/>
229 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
230 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
231 <binary/>
232 </binaryDataArray>
233 </binaryDataArrayList>
234 </spectrum>
235 <spectrum index="6" id="Spectrum=7" defaultArrayLength="38">
236 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
237 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
238 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="304.595254080636" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
239 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
240 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
241 <scanList count="1">
242 <scan>
243 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
244 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
245 </scan>
246 </scanList>
247 <binaryDataArrayList count="2">
248 <binaryDataArray encodedLength="0">
249 <referenceableParamGroupRef ref="mzArray"/>
250 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="3184"/>
251 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
252 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
253 <binary/>
254 </binaryDataArray>
255 <binaryDataArray encodedLength="0">
256 <referenceableParamGroupRef ref="intensityArray"/>
257 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="3488"/>
258 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
259 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
260 <binary/>
261 </binaryDataArray>
262 </binaryDataArrayList>
263 </spectrum>
264 <spectrum index="7" id="Spectrum=8" defaultArrayLength="33">
265 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
266 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
267 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="306.32292175293" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
268 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
269 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
270 <scanList count="1">
271 <scan>
272 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
273 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
274 </scan>
275 </scanList>
276 <binaryDataArrayList count="2">
277 <binaryDataArray encodedLength="0">
278 <referenceableParamGroupRef ref="mzArray"/>
279 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="3792"/>
280 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
281 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
282 <binary/>
283 </binaryDataArray>
284 <binaryDataArray encodedLength="0">
285 <referenceableParamGroupRef ref="intensityArray"/>
286 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4056"/>
287 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
288 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
289 <binary/>
290 </binaryDataArray>
291 </binaryDataArrayList>
292 </spectrum>
293 <spectrum index="8" id="Spectrum=9" defaultArrayLength="28">
294 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
295 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
296 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="328.937515258789" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
297 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="396.916674804687" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
298 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
299 <scanList count="1">
300 <scan>
301 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
302 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
303 </scan>
304 </scanList>
305 <binaryDataArrayList count="2">
306 <binaryDataArray encodedLength="0">
307 <referenceableParamGroupRef ref="mzArray"/>
308 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4320"/>
309 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
310 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
311 <binary/>
312 </binaryDataArray>
313 <binaryDataArray encodedLength="0">
314 <referenceableParamGroupRef ref="intensityArray"/>
315 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4544"/>
316 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
317 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
318 <binary/>
319 </binaryDataArray>
320 </binaryDataArrayList>
321 </spectrum>
322 </spectrumList>
323 </run>
324 </mzML>