Mercurial > repos > galaxyp > cardinal_preprocessing

annotate test-data/out3.imzml @ 2:1b875f0b8024 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
author galaxyp
date Fri, 15 Feb 2019 10:22:14 -0500
parents
children 5bf056c0354e
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2
1b875f0b8024 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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1 <?xml version="1.0"?>
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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">
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3 <cvList count="3">
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4 <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />
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5 <cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />
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6 <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />
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7 </cvList>
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8 <fileDescription>
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9 <fileContent>
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10 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
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11 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
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12 <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{AEDF2DEE-A321-4DAF-B971-943AE2AF79A6}" />
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13 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="8311A159EC925605745E409F14BB6C570FF59ACA" />
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14 <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
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15 </fileContent>
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16 </fileDescription>
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17 <referenceableParamGroupList count="4">
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18 <referenceableParamGroup id="spectrum1">
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19 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
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20 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />
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21 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
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22 </referenceableParamGroup>
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23 <referenceableParamGroup id="scan1">
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24 <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
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25 <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
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26 </referenceableParamGroup>
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27 <referenceableParamGroup id="mzArray">
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28 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
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29 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
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30 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
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31 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
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32 </referenceableParamGroup>
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33 <referenceableParamGroup id="intensityArray">
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34 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
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35 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
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36 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
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37 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
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38 </referenceableParamGroup>
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39 </referenceableParamGroupList>
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40 <sampleList count="1">
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41 <sample id="sample1" name="Sample1">
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42 <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />
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43 </sample>
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44 </sampleList>
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45 <softwareList count="1">
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46 <software id="Cardinal" version="1.12.1">
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47 <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
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48 </software>
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49 </softwareList>
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50 <scanSettingsList count="1">
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51 <scanSettings id="scansettings1">
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52 <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
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53 <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="2" />
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54 </scanSettings>
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55 </scanSettingsList>
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56 <instrumentConfigurationList count="1">
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57 <instrumentConfiguration id="IC1" />
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58 </instrumentConfigurationList>
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59 <dataProcessingList count="1">
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60 <dataProcessing id="CardinalWriteImzML">
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61 <processingMethod order="1" softwareRef="Cardinal">
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62 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />
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63 </processingMethod>
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64 </dataProcessing>
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65 </dataProcessingList>
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66 <run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">
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67 <spectrumList count="3" defaultDataProcessingRef="CardinalWriteImzML">
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68 <spectrum id="Spectrum=1" defaultArrayLength="0" index="1">
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69 <referenceableParamGroupRef ref="spectrum1" />
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70 <scanList count="1">
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72 <scan instrumentConfigurationRef="IC1">
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73 <referenceableParamGroupRef ref="scan1" />
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75 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
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76 </scan>
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77 </scanList>
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78 <binaryDataArrayList count="2">
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79 <binaryDataArray encodedLength="0">
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80 <referenceableParamGroupRef ref="mzArray" />
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