annotate test-data/outfile2.imzml @ 4:e9300ef37403 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
author galaxyp
date Fri, 22 Mar 2019 08:26:23 -0400
parents 36d38d2cf88c
children
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36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <mzML 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.xsd" id="out" version="1.1.0">
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3 <cvList count="2">
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4 <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.44.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
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5 <cv id="UO" fullName="Unit Ontology" version="12:10:2012" URI="http://obo.cvs.sourceforge.net/*checkout*/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"/>
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11 <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{54a5519e-643b-4eb1-b82b-d55aaa5e9015}"/>
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12 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="12d68eada8b274b1bba9520cef0ff98d6fc95bf4"/>
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13 <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous"/>
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14 <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/>
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15 </fileContent>
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16 </fileDescription>
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17 <softwareList count="1">
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18 <software id="MALDIquantForeign" version="0.11.5"/>
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19 </softwareList>
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20 <referenceableParamGroupList count="2">
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21 <referenceableParamGroup id="mzArray">
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22 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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23 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
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24 <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
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25 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
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26 </referenceableParamGroup>
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27 <referenceableParamGroup id="intensityArray">
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28 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
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29 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
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30 <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
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31 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
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32 </referenceableParamGroup>
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33 </referenceableParamGroupList>
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34 <scanSettingsList count="1">
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35 <scanSettings id="scansetting1">
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36 <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="1"/>
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37 <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3"/>
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38 <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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39 <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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40 <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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41 <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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42 </scanSettings>
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43 </scanSettingsList>
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44 <instrumentConfigurationList count="1">
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45 <instrumentConfiguration id="IC0"/>
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46 </instrumentConfigurationList>
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47 <dataProcessingList count="1">
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48 <dataProcessing id="export">
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49 <processingMethod order="1" softwareRef="MALDIquantForeign">
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50 <userParam name="MALDIquant object(s) exported to mzML" value=""/>
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51 </processingMethod>
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52 </dataProcessing>
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53 </dataProcessingList>
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54 <run id="run0" defaultInstrumentConfigurationRef="IC0">
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55 <spectrumList count="2" defaultDataProcessingRef="export">
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56 <spectrum index="0" id="scan=0" defaultArrayLength="8399">
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57 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
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58 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
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59 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="100.000007629395" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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60 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="799.816687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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61 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
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62 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="16.7431673605698"/>
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63 <scanList count="1">
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64 <scan>
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65 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
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66 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
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67 </scan>
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68 </scanList>
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69 <binaryDataArrayList count="2">
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70 <binaryDataArray encodedLength="0">
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71 <referenceableParamGroupRef ref="mzArray"/>
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72 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
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73 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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74 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
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75 <binary/>
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76 </binaryDataArray>
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77 <binaryDataArray encodedLength="0">
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78 <referenceableParamGroupRef ref="intensityArray"/>
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79 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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80 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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81 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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82 <binary/>
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83 </binaryDataArray>
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84 </binaryDataArrayList>
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85 </spectrum>
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86 <spectrum index="1" id="scan=1" defaultArrayLength="8399">
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87 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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88 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
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89 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="100.083335876465" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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90 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="799.9" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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91 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
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92 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="10.6534160746182"/>
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93 <scanList count="1">
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94 <scan>
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95 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
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96 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
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97 </scan>
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98 </scanList>
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99 <binaryDataArrayList count="2">
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100 <binaryDataArray encodedLength="0">
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101 <referenceableParamGroupRef ref="mzArray"/>
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102 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
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103 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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104 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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105 <binary/>
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106 </binaryDataArray>
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107 <binaryDataArray encodedLength="0">
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108 <referenceableParamGroupRef ref="intensityArray"/>
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109 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400"/>
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110 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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111 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="67192"/>
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112 <binary/>
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113 </binaryDataArray>
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114 </binaryDataArrayList>
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115 </spectrum>
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116 </spectrumList>
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117 </run>
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118 </mzML>