Mercurial > repos > galaxyp > msconvert

annotate test-data/BrukerBafTest.mzML @ 10:9d5de24e6ef7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
author galaxyp
date Sat, 23 Feb 2019 06:25:48 -0500
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children 6153e8ada1ee
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10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <indexedmzML 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/mzML1.1.2_idx.xsd">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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3 <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="BrukerBafTest" version="1.1.0">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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4 <cvList count="2">
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5 <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
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6 <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.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 </fileContent>
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12 <sourceFileList count="1">
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13 <sourceFile id="BrukerBafTest.d_x005c_Analysis.baf" name="Analysis.baf" location="file:///">
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14 <cvParam cvRef="MS" accession="MS:1000772" name="Bruker BAF nativeID format" value=""/>
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15 <cvParam cvRef="MS" accession="MS:1000815" name="Bruker BAF format" value=""/>
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16 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="5e1b8f06983c2e671a4a96714721c327f1e67ee1"/>
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17 </sourceFile>
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18 </sourceFileList>
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19 </fileDescription>
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20 <referenceableParamGroupList count="1">
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21 <referenceableParamGroup id="CommonInstrumentParams">
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22 <cvParam cvRef="MS" accession="MS:1001556" name="Bruker Daltonics apex series" value=""/>
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23 </referenceableParamGroup>
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24 </referenceableParamGroupList>
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25 <softwareList count="3">
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26 <software id="BAF2SQL" version="2.7.300.20-112">
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27 <cvParam cvRef="MS" accession="MS:1000692" name="Bruker software" value=""/>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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28 <userParam name="software name" value="BAF2SQL"/>
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29 </software>
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30 <software id="apexControl" version="ApexControl 3.0.0.alpha.35 (development version, April 18, 2008)">
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31 <cvParam cvRef="MS" accession="MS:1000706" name="apexControl" value=""/>
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32 </software>
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33 <software id="pwiz_Reader_Bruker" version="3.0.19044">
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34 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
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35 </software>
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36 </softwareList>
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37 <instrumentConfigurationList count="1">
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38 <instrumentConfiguration id="IC1">
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39 <referenceableParamGroupRef ref="CommonInstrumentParams"/>
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40 <componentList count="3">
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41 <source order="1">
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42 <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
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43 <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/>
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44 </source>
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45 <analyzer order="2">
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46 <cvParam cvRef="MS" accession="MS:1000079" name="fourier transform ion cyclotron resonance mass spectrometer" value=""/>
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47 </analyzer>
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48 <detector order="3">
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49 <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>
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50 </detector>
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51 </componentList>
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52 <softwareRef ref="apexControl"/>
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53 </instrumentConfiguration>
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54 </instrumentConfigurationList>
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55 <dataProcessingList count="1">
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56 <dataProcessing id="pwiz_Reader_Bruker_conversion">
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57 <processingMethod order="0" softwareRef="pwiz_Reader_Bruker">
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58 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
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59 </processingMethod>
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60 <processingMethod order="1" softwareRef="pwiz_Reader_Bruker">
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61 <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
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62 <userParam name="Bruker/Agilent/CompassXtract peak picking"/>
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63 </processingMethod>
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64 </dataProcessing>
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65 </dataProcessingList>
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66 <run id="BrukerBafTest" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2008-11-04T10:55:29Z" defaultSourceFileRef="BrukerBafTest.d_x005c_Analysis.baf">
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67 <spectrumList count="1" defaultDataProcessingRef="pwiz_Reader_Bruker_conversion">
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68 <spectrum index="0" id="scan=1" defaultArrayLength="71">
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69 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
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70 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
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71 <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
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72 <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="7.81485056e08"/>
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73 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="5.704013312e09"/>
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74 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
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75 <scanList count="1">
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76 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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77 <scan>
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78 <scanWindowList count="1">
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79 <scanWindow>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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80 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="347.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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81 <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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82 </scanWindow>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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83 </scanWindowList>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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84 </scan>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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85 </scanList>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
86 <binaryDataArrayList count="2">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
87 <binaryDataArray encodedLength="744">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
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88 <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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89 <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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90 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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91 <binary>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</binary>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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92 </binaryDataArray>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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93 <binaryDataArray encodedLength="396">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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94 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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95 <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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96 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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97 <binary>eJwBHAHj/rDDDUyYqRlNHLfVSxCnz0tc0wNLIDP1SmBcI0wQODFMYEmGTYgzNkswU3FNYM99S4DvDEuAMXBNgDszTPB3ik3gYWBMcEOoS2DxQ0sgjjlLgEhLS6D3jUug3GJNUHMlToAmSkwAz7RLAKpPSwBFDkuAY2dLIGWbTID6CU0AvElLAB7zSmCQKkuAQKVLQIj0S+Bbk0wQUjpO4L3LS6C+kEvAXiNLwKgTS8DUMkxg5m5MoNNNTaD2gE3gcihLIA9ES2C5iUuAQARLQIwES4BHNEuA7qdLwMYuS4AHeEvAxgtLwKW6S8BuokvAQVpMQC09TEAwnUvAXlNNAHxfSyALAE2AYt5LgAduS8Ayvk2Ao1hLwAIsSwDi9EqAPGFLsyVy9w==</binary>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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98 </binaryDataArray>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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99 </binaryDataArrayList>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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100 </spectrum>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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101 </spectrumList>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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102 </run>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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103 </mzML>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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104 <indexList count="2">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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105 <index name="spectrum">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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106 <offset idRef="scan=1">4166</offset>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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107 </index>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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108 <index name="chromatogram">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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109 </index>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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110 </indexList>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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111 <indexListOffset>7590</indexListOffset>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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112 <fileChecksum>e6b4d51fdbe306f0823fe1cb583e7ec52629303f</fileChecksum>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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113 </indexedmzML>