Mercurial > repos > galaxyp > cardinal_single_ion_segmentation
comparison test-data/out3.imzml @ 0:4cb6c83d3777 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441"
| author | galaxyp |
|---|---|
| date | Tue, 22 Feb 2022 20:51:09 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:4cb6c83d3777 |
|---|---|
| 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="97f42eea-750c-49e4-b46d-08c548dc3b9d" /> | |
| 13 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4e046226f81e9c78255df625ca3546ef26dd0693" /> | |
| 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 </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="2.6.0"> | |
| 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:1000042" name="max count of pixel x" value="3" /> | |
| 52 <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="1" /> | |
| 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="2" /> | |
| 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="Inf" /> | |
| 57 </scanSettings> | |
| 58 </scanSettingsList> | |
| 59 <instrumentConfigurationList count="1"> | |
| 60 <instrumentConfiguration id="IC1"> | |
| 61 <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" /> | |
| 62 </instrumentConfiguration> | |
| 63 </instrumentConfigurationList> | |
| 64 <dataProcessingList count="1"> | |
| 65 <dataProcessing id="CardinalWriteImzML"> | |
| 66 <processingMethod order="1" softwareRef="Cardinal"> | |
| 67 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" /> | |
| 68 </processingMethod> | |
| 69 </dataProcessing> | |
| 70 </dataProcessingList> | |
| 71 <run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1"> | |
| 72 <spectrumList count="3" defaultDataProcessingRef="CardinalWriteImzML"> | |
| 73 <spectrum id="Spectrum=1" defaultArrayLength="0" index="1"> | |
| 74 <referenceableParamGroupRef ref="spectrum1" /> | |
| 75 <scanList count="1"> | |
| 76 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> | |
| 77 <scan instrumentConfigurationRef="IC1"> | |
| 78 <referenceableParamGroupRef ref="scan1" /> | |
| 79 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> | |
| 80 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> | |
| 81 <userParam name="3DPositionX" value="1.000000" /> | |
| 82 <userParam name="3DPositionY" value="2.000000" /> | |
| 83 </scan> | |
| 84 </scanList> | |
| 85 <binaryDataArrayList count="2"> | |
| 86 <binaryDataArray encodedLength="0"> | |
| 87 <referenceableParamGroupRef ref="mzArray" /> | |
| 88 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> | |
| 89 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" /> | |
| 90 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" /> | |
| 91 <binary /> | |
| 92 </binaryDataArray> | |
| 93 <binaryDataArray encodedLength="0"> | |
| 94 <referenceableParamGroupRef ref="intensityArray" /> | |
| 95 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="2416" /> | |
| 96 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" /> | |
| 97 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" /> | |
| 98 <binary /> | |
| 99 </binaryDataArray> | |
| 100 </binaryDataArrayList> | |
| 101 </spectrum> | |
| 102 <spectrum id="Spectrum=2" defaultArrayLength="0" index="2"> | |
| 103 <referenceableParamGroupRef ref="spectrum1" /> | |
| 104 <scanList count="1"> | |
| 105 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> | |
| 106 <scan instrumentConfigurationRef="IC1"> | |
| 107 <referenceableParamGroupRef ref="scan1" /> | |
| 108 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> | |
| 109 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> | |
| 110 <userParam name="3DPositionX" value="2.000000" /> | |
| 111 <userParam name="3DPositionY" value="2.000000" /> | |
| 112 </scan> | |
| 113 </scanList> | |
| 114 <binaryDataArrayList count="2"> | |
| 115 <binaryDataArray encodedLength="0"> | |
| 116 <referenceableParamGroupRef ref="mzArray" /> | |
| 117 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> | |
| 118 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" /> | |
| 119 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" /> | |
| 120 <binary /> | |
| 121 </binaryDataArray> | |
| 122 <binaryDataArray encodedLength="0"> | |
| 123 <referenceableParamGroupRef ref="intensityArray" /> | |
| 124 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4816" /> | |
| 125 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" /> | |
| 126 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" /> | |
| 127 <binary /> | |
| 128 </binaryDataArray> | |
| 129 </binaryDataArrayList> | |
| 130 </spectrum> | |
| 131 <spectrum id="Spectrum=3" defaultArrayLength="0" index="3"> | |
| 132 <referenceableParamGroupRef ref="spectrum1" /> | |
| 133 <scanList count="1"> | |
| 134 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> | |
| 135 <scan instrumentConfigurationRef="IC1"> | |
| 136 <referenceableParamGroupRef ref="scan1" /> | |
| 137 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> | |
| 138 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> | |
| 139 <userParam name="3DPositionX" value="3.000000" /> | |
| 140 <userParam name="3DPositionY" value="2.000000" /> | |
| 141 </scan> | |
| 142 </scanList> | |
| 143 <binaryDataArrayList count="2"> | |
| 144 <binaryDataArray encodedLength="0"> | |
| 145 <referenceableParamGroupRef ref="mzArray" /> | |
| 146 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> | |
| 147 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" /> | |
| 148 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" /> | |
| 149 <binary /> | |
| 150 </binaryDataArray> | |
| 151 <binaryDataArray encodedLength="0"> | |
| 152 <referenceableParamGroupRef ref="intensityArray" /> | |
| 153 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="7216" /> | |
| 154 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" /> | |
| 155 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" /> | |
| 156 <binary /> | |
| 157 </binaryDataArray> | |
| 158 </binaryDataArrayList> | |
| 159 </spectrum> | |
| 160 </spectrumList> | |
| 161 </run> | |
| 162 </mzML> |