Mercurial > repos > galaxyp > cardinal_mz_images

annotate test-data/112_auto_combined.imzml @ 5:4a05e47cd0ea draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
author galaxyp
date Fri, 13 Dec 2019 13:51:29 -0500
parents 27a4c660bbca
children 5e6f8fb2df07
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27a4c660bbca 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"?>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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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">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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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" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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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" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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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>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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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="" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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11 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
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4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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12 <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="a0620366-fee2-4a2a-a643-0f0e0c9ae5a6" />
4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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14 <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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15 </fileContent>
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16 </fileDescription>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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17 <referenceableParamGroupList count="4">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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18 <referenceableParamGroup id="spectrum1">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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19 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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20 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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21 <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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22 </referenceableParamGroup>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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23 <referenceableParamGroup id="scan1">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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24 <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
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25 </referenceableParamGroup>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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26 <referenceableParamGroup id="mzArray">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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27 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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28 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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31 </referenceableParamGroup>
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32 <referenceableParamGroup id="intensityArray">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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33 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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34 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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35 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
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4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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36 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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37 </referenceableParamGroup>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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38 </referenceableParamGroupList>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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39 <sampleList count="1">
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40 <sample id="sample1" name="Sample1">
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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41 <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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42 </sample>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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43 </sampleList>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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44 <softwareList count="1">
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4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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45 <software id="Cardinal" version="2.2.6">
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46 <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
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47 </software>
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48 </softwareList>
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49 <scanSettingsList count="1">
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50 <scanSettings id="scansettings1">
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4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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51 <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="5" />
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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52 <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
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4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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53 <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="15" />
4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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57 </scanSettings>
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58 </scanSettingsList>
27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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59 <instrumentConfigurationList count="1">
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4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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60 <instrumentConfiguration id="IC1">
4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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61 <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
4a05e47cd0ea "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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62 </instrumentConfiguration>
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63 </instrumentConfigurationList>
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64 <dataProcessingList count="1">
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65 <dataProcessing id="CardinalWriteImzML">
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66 <processingMethod order="1" softwareRef="Cardinal">
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67 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />
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68 </processingMethod>
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69 </dataProcessing>
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70 </dataProcessingList>
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71 <run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">
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72 <spectrumList count="15" defaultDataProcessingRef="CardinalWriteImzML">
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73 <spectrum id="Spectrum=1" defaultArrayLength="0" index="1">
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74 <referenceableParamGroupRef ref="spectrum1" />
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75 <scanList count="1">
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77 <scan instrumentConfigurationRef="IC1">
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78 <referenceableParamGroupRef ref="scan1" />
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80 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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galaxyp
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galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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galaxyp
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galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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galaxyp
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galaxyp
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galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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galaxyp
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galaxyp
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galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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galaxyp
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diff changeset
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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27a4c660bbca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
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