Mercurial > repos > galaxyp > cardinal_preprocessing

comparison test-data/out7.imzml @ 6:5bf056c0354e 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 15e24b1f0143679647906bc427654f66b417a45c"
author galaxyp
date Wed, 25 Mar 2020 08:13:17 -0400
parents 1b875f0b8024
children ca727a6dede6
comparison
equal deleted inserted replaced
5:ed9ed1e6cca2 6:5bf056c0354e
7 </cvList> 7 </cvList>
8 <fileDescription> 8 <fileDescription>
9 <fileContent> 9 <fileContent>
10 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> 10 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
11 <cvParam cvRef="MS" accession="MS:1000128" name="profile 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="{B095BB77-684D-4BFF-82D3-B76D0EB1C0CD}" /> 12 <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="bf61653e-aa1a-4f9a-a84d-3ff3435ee7fe" />
13 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="628A551B81DCF301B65E3A5AB1182F0BF319533C" /> 13 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="352c33defde6728b7dfb83e18ed1c433fa4b8697" />
14 <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> 14 <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
15 </fileContent> 15 </fileContent>
16 </fileDescription> 16 </fileDescription>
17 <referenceableParamGroupList count="4"> 17 <referenceableParamGroupList count="4">
18 <referenceableParamGroup id="spectrum1"> 18 <referenceableParamGroup id="spectrum1">
20 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" /> 20 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />
21 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> 21 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
22 </referenceableParamGroup> 22 </referenceableParamGroup>
23 <referenceableParamGroup id="scan1"> 23 <referenceableParamGroup id="scan1">
24 <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" /> 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> 25 </referenceableParamGroup>
27 <referenceableParamGroup id="mzArray"> 26 <referenceableParamGroup id="mzArray">
28 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> 27 <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" /> 28 <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" /> 29 <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" /> 30 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
32 </referenceableParamGroup> 31 </referenceableParamGroup>
33 <referenceableParamGroup id="intensityArray"> 32 <referenceableParamGroup id="intensityArray">
34 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> 33 <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" /> 34 <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" /> 35 <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" /> 36 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
38 </referenceableParamGroup> 37 </referenceableParamGroup>
39 </referenceableParamGroupList> 38 </referenceableParamGroupList>
40 <sampleList count="1"> 39 <sampleList count="1">
41 <sample id="sample1" name="Sample1"> 40 <sample id="sample1" name="Sample1">
42 <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" /> 41 <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />
43 </sample> 42 </sample>
44 </sampleList> 43 </sampleList>
45 <softwareList count="1"> 44 <softwareList count="1">
46 <software id="Cardinal" version="1.12.1"> 45 <software id="Cardinal" version="2.4.0">
47 <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> 46 <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
48 </software> 47 </software>
49 </softwareList> 48 </softwareList>
50 <scanSettingsList count="1"> 49 <scanSettingsList count="1">
51 <scanSettings id="scansettings1"> 50 <scanSettings id="scansettings1">
52 <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" /> 51 <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" /> 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="3" />
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" />
54 </scanSettings> 57 </scanSettings>
55 </scanSettingsList> 58 </scanSettingsList>
56 <instrumentConfigurationList count="1"> 59 <instrumentConfigurationList count="1">
57 <instrumentConfiguration id="IC1" /> 60 <instrumentConfiguration id="IC1">
61 <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
62 </instrumentConfiguration>
58 </instrumentConfigurationList> 63 </instrumentConfigurationList>
59 <dataProcessingList count="1"> 64 <dataProcessingList count="1">
60 <dataProcessing id="CardinalWriteImzML"> 65 <dataProcessing id="CardinalWriteImzML">
61 <processingMethod order="1" softwareRef="Cardinal"> 66 <processingMethod order="1" softwareRef="Cardinal">
62 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" /> 67 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />
71 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> 76 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
72 <scan instrumentConfigurationRef="IC1"> 77 <scan instrumentConfigurationRef="IC1">
73 <referenceableParamGroupRef ref="scan1" /> 78 <referenceableParamGroupRef ref="scan1" />
74 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> 79 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
75 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> 80 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
81 <userParam name="3DPositionX" value="1.000000" />
82 <userParam name="3DPositionY" value="1.000000" />
76 </scan> 83 </scan>
77 </scanList> 84 </scanList>
78 <binaryDataArrayList count="2"> 85 <binaryDataArrayList count="2">
79 <binaryDataArray encodedLength="0"> 86 <binaryDataArray encodedLength="0">
80 <referenceableParamGroupRef ref="mzArray" /> 87 <referenceableParamGroupRef ref="mzArray" />
98 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> 105 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
99 <scan instrumentConfigurationRef="IC1"> 106 <scan instrumentConfigurationRef="IC1">
100 <referenceableParamGroupRef ref="scan1" /> 107 <referenceableParamGroupRef ref="scan1" />
101 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> 108 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
102 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> 109 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
110 <userParam name="3DPositionX" value="2.000000" />
111 <userParam name="3DPositionY" value="1.000000" />
103 </scan> 112 </scan>
104 </scanList> 113 </scanList>
105 <binaryDataArrayList count="2"> 114 <binaryDataArrayList count="2">
106 <binaryDataArray encodedLength="0"> 115 <binaryDataArray encodedLength="0">
107 <referenceableParamGroupRef ref="mzArray" /> 116 <referenceableParamGroupRef ref="mzArray" />
125 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> 134 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
126 <scan instrumentConfigurationRef="IC1"> 135 <scan instrumentConfigurationRef="IC1">
127 <referenceableParamGroupRef ref="scan1" /> 136 <referenceableParamGroupRef ref="scan1" />
128 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> 137 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
129 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> 138 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
139 <userParam name="3DPositionX" value="3.000000" />
140 <userParam name="3DPositionY" value="1.000000" />
130 </scan> 141 </scan>
131 </scanList> 142 </scanList>
132 <binaryDataArrayList count="2"> 143 <binaryDataArrayList count="2">
133 <binaryDataArray encodedLength="0"> 144 <binaryDataArray encodedLength="0">
134 <referenceableParamGroupRef ref="mzArray" /> 145 <referenceableParamGroupRef ref="mzArray" />
152 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> 163 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
153 <scan instrumentConfigurationRef="IC1"> 164 <scan instrumentConfigurationRef="IC1">
154 <referenceableParamGroupRef ref="scan1" /> 165 <referenceableParamGroupRef ref="scan1" />
155 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> 166 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
156 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> 167 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
168 <userParam name="3DPositionX" value="1.000000" />
169 <userParam name="3DPositionY" value="2.000000" />
157 </scan> 170 </scan>
158 </scanList> 171 </scanList>
159 <binaryDataArrayList count="2"> 172 <binaryDataArrayList count="2">
160 <binaryDataArray encodedLength="0"> 173 <binaryDataArray encodedLength="0">
161 <referenceableParamGroupRef ref="mzArray" /> 174 <referenceableParamGroupRef ref="mzArray" />
179 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> 192 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
180 <scan instrumentConfigurationRef="IC1"> 193 <scan instrumentConfigurationRef="IC1">
181 <referenceableParamGroupRef ref="scan1" /> 194 <referenceableParamGroupRef ref="scan1" />
182 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> 195 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
183 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> 196 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
197 <userParam name="3DPositionX" value="2.000000" />
198 <userParam name="3DPositionY" value="2.000000" />
184 </scan> 199 </scan>
185 </scanList> 200 </scanList>
186 <binaryDataArrayList count="2"> 201 <binaryDataArrayList count="2">
187 <binaryDataArray encodedLength="0"> 202 <binaryDataArray encodedLength="0">
188 <referenceableParamGroupRef ref="mzArray" /> 203 <referenceableParamGroupRef ref="mzArray" />
206 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> 221 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
207 <scan instrumentConfigurationRef="IC1"> 222 <scan instrumentConfigurationRef="IC1">
208 <referenceableParamGroupRef ref="scan1" /> 223 <referenceableParamGroupRef ref="scan1" />
209 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> 224 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
210 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> 225 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
226 <userParam name="3DPositionX" value="3.000000" />
227 <userParam name="3DPositionY" value="2.000000" />
211 </scan> 228 </scan>
212 </scanList> 229 </scanList>
213 <binaryDataArrayList count="2"> 230 <binaryDataArrayList count="2">
214 <binaryDataArray encodedLength="0"> 231 <binaryDataArray encodedLength="0">
215 <referenceableParamGroupRef ref="mzArray" /> 232 <referenceableParamGroupRef ref="mzArray" />
233 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> 250 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
234 <scan instrumentConfigurationRef="IC1"> 251 <scan instrumentConfigurationRef="IC1">
235 <referenceableParamGroupRef ref="scan1" /> 252 <referenceableParamGroupRef ref="scan1" />
236 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> 253 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
237 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> 254 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
255 <userParam name="3DPositionX" value="1.000000" />
256 <userParam name="3DPositionY" value="3.000000" />
238 </scan> 257 </scan>
239 </scanList> 258 </scanList>
240 <binaryDataArrayList count="2"> 259 <binaryDataArrayList count="2">
241 <binaryDataArray encodedLength="0"> 260 <binaryDataArray encodedLength="0">
242 <referenceableParamGroupRef ref="mzArray" /> 261 <referenceableParamGroupRef ref="mzArray" />
260 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> 279 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
261 <scan instrumentConfigurationRef="IC1"> 280 <scan instrumentConfigurationRef="IC1">
262 <referenceableParamGroupRef ref="scan1" /> 281 <referenceableParamGroupRef ref="scan1" />
263 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> 282 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
264 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> 283 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
284 <userParam name="3DPositionX" value="2.000000" />
285 <userParam name="3DPositionY" value="3.000000" />
265 </scan> 286 </scan>
266 </scanList> 287 </scanList>
267 <binaryDataArrayList count="2"> 288 <binaryDataArrayList count="2">
268 <binaryDataArray encodedLength="0"> 289 <binaryDataArray encodedLength="0">
269 <referenceableParamGroupRef ref="mzArray" /> 290 <referenceableParamGroupRef ref="mzArray" />
287 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> 308 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
288 <scan instrumentConfigurationRef="IC1"> 309 <scan instrumentConfigurationRef="IC1">
289 <referenceableParamGroupRef ref="scan1" /> 310 <referenceableParamGroupRef ref="scan1" />
290 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> 311 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
291 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> 312 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
313 <userParam name="3DPositionX" value="3.000000" />
314 <userParam name="3DPositionY" value="3.000000" />
292 </scan> 315 </scan>
293 </scanList> 316 </scanList>
294 <binaryDataArrayList count="2"> 317 <binaryDataArrayList count="2">
295 <binaryDataArray encodedLength="0"> 318 <binaryDataArray encodedLength="0">
296 <referenceableParamGroupRef ref="mzArray" /> 319 <referenceableParamGroupRef ref="mzArray" />