Mercurial > repos > galaxyp > cardinal_data_exporter
comparison test-data/Example_Continuous.imzML @ 0:28ba52c9548c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
| author | galaxyp |
|---|---|
| date | Mon, 01 Oct 2018 01:05:33 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:28ba52c9548c |
|---|---|
| 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="{51BB7C6F-9974-4626-B35F-5B65547BAE6B}" /> | |
| 13 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="26C26A63DCF7CD1AD768A67AEDB7131C5D88C397" /> | |
| 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 <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="1.12.0"> | |
| 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="1199" /> | |
| 83 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 84 <binary /> | |
| 85 </binaryDataArray> | |
| 86 <binaryDataArray encodedLength="0"> | |
| 87 <referenceableParamGroupRef ref="intensityArray" /> | |
| 88 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4812" /> | |
| 89 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> | |
| 90 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 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="1199" /> | |
| 110 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 111 <binary /> | |
| 112 </binaryDataArray> | |
| 113 <binaryDataArray encodedLength="0"> | |
| 114 <referenceableParamGroupRef ref="intensityArray" /> | |
| 115 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="9608" /> | |
| 116 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> | |
| 117 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 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="1199" /> | |
| 137 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 138 <binary /> | |
| 139 </binaryDataArray> | |
| 140 <binaryDataArray encodedLength="0"> | |
| 141 <referenceableParamGroupRef ref="intensityArray" /> | |
| 142 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="14404" /> | |
| 143 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> | |
| 144 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 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="1199" /> | |
| 164 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 165 <binary /> | |
| 166 </binaryDataArray> | |
| 167 <binaryDataArray encodedLength="0"> | |
| 168 <referenceableParamGroupRef ref="intensityArray" /> | |
| 169 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="19200" /> | |
| 170 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> | |
| 171 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 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="1199" /> | |
| 191 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 192 <binary /> | |
| 193 </binaryDataArray> | |
| 194 <binaryDataArray encodedLength="0"> | |
| 195 <referenceableParamGroupRef ref="intensityArray" /> | |
| 196 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="23996" /> | |
| 197 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> | |
| 198 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 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="1199" /> | |
| 218 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 219 <binary /> | |
| 220 </binaryDataArray> | |
| 221 <binaryDataArray encodedLength="0"> | |
| 222 <referenceableParamGroupRef ref="intensityArray" /> | |
| 223 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="28792" /> | |
| 224 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> | |
| 225 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 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="1199" /> | |
| 245 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 246 <binary /> | |
| 247 </binaryDataArray> | |
| 248 <binaryDataArray encodedLength="0"> | |
| 249 <referenceableParamGroupRef ref="intensityArray" /> | |
| 250 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33588" /> | |
| 251 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> | |
| 252 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 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="1199" /> | |
| 272 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 273 <binary /> | |
| 274 </binaryDataArray> | |
| 275 <binaryDataArray encodedLength="0"> | |
| 276 <referenceableParamGroupRef ref="intensityArray" /> | |
| 277 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="38384" /> | |
| 278 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> | |
| 279 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 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="1199" /> | |
| 299 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 300 <binary /> | |
| 301 </binaryDataArray> | |
| 302 <binaryDataArray encodedLength="0"> | |
| 303 <referenceableParamGroupRef ref="intensityArray" /> | |
| 304 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="43180" /> | |
| 305 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> | |
| 306 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> | |
| 307 <binary /> | |
| 308 </binaryDataArray> | |
| 309 </binaryDataArrayList> | |
| 310 </spectrum> | |
| 311 </spectrumList> | |
| 312 </run> | |
| 313 </mzML> |
