Mercurial > repos > galaxyp > cardinal_mz_images
comparison test-data/out8.imzml @ 6:25b83cbd596a draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
author | galaxyp |
---|---|
date | Wed, 25 Mar 2020 05:31:15 -0400 |
parents | |
children | 08ebd8da780c |
comparison
equal
deleted
inserted
replaced
5:4a05e47cd0ea | 6:25b83cbd596a |
---|---|
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="ace74b18-25e2-4722-89f4-6eedc2b62ed8" /> | |
13 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="41d580d8acf3e67df8b63f001fe941da7334861b" /> | |
14 <cvParam cvRef="IMS" accession="IMS:1000031" name="processed" 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="2.4.0"> | |
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="2" /> | |
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="2.000000" /> | |
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="5" 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="8399" /> | |
94 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> | |
95 <binary /> | |
96 </binaryDataArray> | |
97 <binaryDataArray encodedLength="0"> | |
98 <referenceableParamGroupRef ref="intensityArray" /> | |
99 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33612" /> | |
100 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> | |
101 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> | |
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="3" /> | |
113 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> | |
114 <userParam name="3DPositionX" value="3.000000" /> | |
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="67208" /> | |
122 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> | |
123 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> | |
124 <binary /> | |
125 </binaryDataArray> | |
126 <binaryDataArray encodedLength="0"> | |
127 <referenceableParamGroupRef ref="intensityArray" /> | |
128 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100804" /> | |
129 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> | |
130 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> | |
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="1" /> | |
142 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> | |
143 <userParam name="3DPositionX" value="1.000000" /> | |
144 <userParam name="3DPositionY" value="2.000000" /> | |
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="134400" /> | |
151 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> | |
152 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> | |
153 <binary /> | |
154 </binaryDataArray> | |
155 <binaryDataArray encodedLength="0"> | |
156 <referenceableParamGroupRef ref="intensityArray" /> | |
157 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996" /> | |
158 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> | |
159 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> | |
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="3" /> | |
171 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> | |
172 <userParam name="3DPositionX" value="3.000000" /> | |
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="201592" /> | |
180 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> | |
181 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> | |
182 <binary /> | |
183 </binaryDataArray> | |
184 <binaryDataArray encodedLength="0"> | |
185 <referenceableParamGroupRef ref="intensityArray" /> | |
186 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188" /> | |
187 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> | |
188 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> | |
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="1" /> | |
200 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> | |
201 <userParam name="3DPositionX" value="1.000000" /> | |
202 <userParam name="3DPositionY" value="3.000000" /> | |
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="268784" /> | |
209 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> | |
210 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> | |
211 <binary /> | |
212 </binaryDataArray> | |
213 <binaryDataArray encodedLength="0"> | |
214 <referenceableParamGroupRef ref="intensityArray" /> | |
215 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380" /> | |
216 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> | |
217 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> | |
218 <binary /> | |
219 </binaryDataArray> | |
220 </binaryDataArrayList> | |
221 </spectrum> | |
222 </spectrumList> | |
223 </run> | |
224 </mzML> |