Mercurial > repos > galaxyp > cardinal_combine

annotate test-data/Example_Processed.imzML @ 4:c1231933bfd6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
author galaxyp
date Fri, 22 Mar 2019 08:09:07 -0400
parents b414378b969f
children
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4
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1 <?xml version="1.0" encoding="ISO-8859-1"?>
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2 <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" xmlns="http://psi.hupo.org/ms/mzml" version="1.1">
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3 <cvList count="4">
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4 <cv URI="http://ontologies.berkeleybop.org/pato.obo" fullName="Phenotype And Trait Ontology" id="PATO" version="releases/2017-07-10"/>
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5 <cv URI="http://ontologies.berkeleybop.org/uo.obo" fullName="Units of Measurement Ontology" id="UO" version="releases/2017-09-25"/>
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6 <cv URI="https://raw.githubusercontent.com/hupo-psi/psi-ms-cv/master/psi-ms.obo" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" id="MS" version="4.1.0"/>
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7 <cv URI="https://raw.githubusercontent.com/imzML/imzML/master/imagingMS.obo" fullName="Mass Spectrometry Imaging Ontology" id="IMS" version="1.1.0"/>
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8 </cvList>
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9 <fileDescription>
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10 <fileContent>
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11 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
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12 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
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13 <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9d501bdc53444916b7e97e795b02c856"/>
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14 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7e8fdb93053915d3edb51b70aa0619ac209964df"/>
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15 <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
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16 </fileContent>
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17 <sourceFileList count="1">
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18 <sourceFile id="sf1" location="C:\Users\Thorsten Schramm\Documents\Promotion\imzML\Website\files\Beispiel-Dateien\Example images\" name="Example.raw">
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19 <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format"/>
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20 <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format"/>
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21 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>
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22 </sourceFile>
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23 </sourceFileList>
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24 <contact>
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25 <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>
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26 <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Institut für Anorganische und Analytische Chemie"/>
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27 <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstraße 60, Haus 16, Gießen, Germany"/>
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28 <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>
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29 </contact>
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30 </fileDescription>
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31 <referenceableParamGroupList count="4">
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32 <referenceableParamGroup id="mzArray">
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33 <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
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34 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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35 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
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36 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
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37 </referenceableParamGroup>
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38 <referenceableParamGroup id="intensityArray">
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39 <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
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40 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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41 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
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42 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
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43 </referenceableParamGroup>
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44 <referenceableParamGroup id="scan1">
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45 <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan"/>
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46 <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/>
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47 </referenceableParamGroup>
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48 <referenceableParamGroup id="spectrum1">
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49 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
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50 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
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51 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
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52 <cvParam cvRef="MS" accession="MS:1000129" name="negative scan"/>
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53 </referenceableParamGroup>
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54 </referenceableParamGroupList>
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55 <sampleList count="1">
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56 <sample id="sample1" name="Sample1">
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57 <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1"/>
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58 </sample>
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59 </sampleList>
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60 <softwareList count="2">
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61 <software id="Xcalibur" version="2.2">
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62 <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur"/>
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63 </software>
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64 <software id="TMC" version="1.1 beta">
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65 <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value=""/>
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66 </software>
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67 </softwareList>
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68 <scanSettingsList count="1">
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69 <scanSettings id="scansettings1">
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70 <cvParam cvRef="IMS" accession="IMS:1000401" name="top down"/>
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71 <cvParam cvRef="IMS" accession="IMS:1000413" name="flyback"/>
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72 <cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan"/>
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73 <cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right"/>
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74 <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixels x" value="3"/>
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75 <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixels y" value="3"/>
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76 <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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80 </scanSettings>
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99 </source>
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100 <analyzer order="2">
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103 </analyzer>
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104 <detector order="3">
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107 </detector>
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109 <softwareRef ref="Xcalibur"/>
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110 </instrumentConfiguration>
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111 </instrumentConfigurationList>
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112 <dataProcessingList count="2">
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113 <dataProcessing id="XcaliburProcessing">
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114 <processingMethod softwareRef="Xcalibur" order="1">
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115 <cvParam cvRef="MS" accession="MS:1000594" name="low intensity data point removal"/>
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116 </processingMethod>
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117 </dataProcessing>
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118 <dataProcessing id="TMCConversion">
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119 <processingMethod softwareRef="TMC" order="2">
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120 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML"/>
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121 </processingMethod>
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122 </dataProcessing>
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123 </dataProcessingList>
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124 <run defaultInstrumentConfigurationRef="LTQFTUltra0" defaultSourceFileRef="sf1" id="Experiment01" sampleRef="sample1" startTimeStamp="2009-08-11T15:59:44">
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125 <spectrumList count="9" defaultDataProcessingRef="XcaliburProcessing">
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126 <spectrum id="Scan=1" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="0">
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127 <referenceableParamGroupRef ref="spectrum1"/>
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128 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="121.85039039868471"/>
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129 <scanList count="1">
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131 <scan instrumentConfigurationRef="LTQFTUltra0">
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132 <referenceableParamGroupRef ref="scan1"/>
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133 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
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135 </scan>
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136 </scanList>
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137 <binaryDataArrayList count="2">
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138 <binaryDataArray encodedLength="0">
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139 <referenceableParamGroupRef ref="mzArray"/>
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140 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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143 <binary />
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144 </binaryDataArray>
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145 <binaryDataArray encodedLength="0">
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146 <referenceableParamGroupRef ref="intensityArray"/>
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147 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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149 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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150 <binary />
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152 </binaryDataArrayList>
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153 </spectrum>
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154 <spectrum id="Scan=2" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="1">
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155 <referenceableParamGroupRef ref="spectrum1"/>
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156 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="182.31835420101888"/>
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157 <scanList count="1">
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327 <scan instrumentConfigurationRef="LTQFTUltra0">
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328 <referenceableParamGroupRef ref="scan1"/>
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329 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
c1231933bfd6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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330 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
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331 </scan>
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332 </scanList>
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333 <binaryDataArrayList count="2">
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334 <binaryDataArray encodedLength="0">
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335 <referenceableParamGroupRef ref="mzArray"/>
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336 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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337 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="470360"/>
c1231933bfd6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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338 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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339 <binary />
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340 </binaryDataArray>
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341 <binaryDataArray encodedLength="0">
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342 <referenceableParamGroupRef ref="intensityArray"/>
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343 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
c1231933bfd6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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344 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="503956"/>
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345 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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346 <binary />
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347 </binaryDataArray>
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348 </binaryDataArrayList>
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349 </spectrum>
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350 <spectrum id="Scan=9" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="8">
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351 <referenceableParamGroupRef ref="spectrum1"/>
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352 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="243.5395066031077"/>
c1231933bfd6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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353 <scanList count="1">
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354 <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
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355 <scan instrumentConfigurationRef="LTQFTUltra0">
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356 <referenceableParamGroupRef ref="scan1"/>
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357 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
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358 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
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359 </scan>
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360 </scanList>
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361 <binaryDataArrayList count="2">
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362 <binaryDataArray encodedLength="0">
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363 <referenceableParamGroupRef ref="mzArray"/>
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364 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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365 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="537552"/>
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366 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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367 <binary />
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368 </binaryDataArray>
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369 <binaryDataArray encodedLength="0">
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370 <referenceableParamGroupRef ref="intensityArray"/>
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371 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
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372 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="571148"/>
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373 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
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374 <binary />
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375 </binaryDataArray>
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376 </binaryDataArrayList>
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377 </spectrum>
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378 </spectrumList>
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379 </run>
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380 </mzML>