Mercurial > repos > galaxyp > maldi_quant_preprocessing

annotate test-data/peak_detection3.imzml @ 4:60ee8c592b13 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
author galaxyp
date Sat, 04 Mar 2023 19:14:31 +0000
parents 71411ac28268
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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"/>
4
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11 <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{dfd6eff6-f7b3-46ec-bf1e-bbb5223f935b}"/>
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12 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1abaedcd2dfe09f9c9c758e03f93a9df0bf815d3"/>
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13 <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
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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 <sourceFileList count="1">
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17 <sourceFile id="SF1" location="/tmp/tmp7arrd4fa/job_working_directory/000/14/working" name="infile.imzML">
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18 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="0d2ad51f69d7b5df0f4d2b2a47b17478f2fca509"/>
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19 </sourceFile>
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20 </sourceFileList>
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21 </fileDescription>
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22 <softwareList count="1">
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23 <software id="MALDIquantForeign" version="0.13"/>
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24 </softwareList>
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25 <referenceableParamGroupList count="2">
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26 <referenceableParamGroup id="mzArray">
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27 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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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:1000523" name="64-bit float" value=""/>
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30 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
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31 </referenceableParamGroup>
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32 <referenceableParamGroup id="intensityArray">
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33 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
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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:1000523" name="64-bit float" value=""/>
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36 <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
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37 </referenceableParamGroup>
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38 </referenceableParamGroupList>
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39 <scanSettingsList count="1">
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40 <scanSettings id="scansetting1">
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41 <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3"/>
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42 <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3"/>
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43 <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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44 <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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45 <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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46 <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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47 </scanSettings>
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48 </scanSettingsList>
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49 <instrumentConfigurationList count="1">
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50 <instrumentConfiguration id="IC0"/>
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51 </instrumentConfigurationList>
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52 <dataProcessingList count="1">
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53 <dataProcessing id="export">
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54 <processingMethod order="1" softwareRef="MALDIquantForeign">
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55 <userParam name="MALDIquant object(s) exported to mzML" value=""/>
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56 </processingMethod>
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57 </dataProcessing>
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58 </dataProcessingList>
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59 <run id="run0" defaultInstrumentConfigurationRef="IC0">
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60 <spectrumList count="9" defaultDataProcessingRef="export">
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61 <spectrum index="0" id="Spectrum=1" defaultArrayLength="9">
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62 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
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63 <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
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64 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="304.166687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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65 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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66 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
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67 <scanList count="1">
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68 <scan>
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69 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
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70 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
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71 </scan>
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72 </scanList>
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73 <binaryDataArrayList count="2">
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74 <binaryDataArray encodedLength="0">
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75 <referenceableParamGroupRef ref="mzArray"/>
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76 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
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77 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="9"/>
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galaxyp
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galaxyp
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galaxyp
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galaxyp
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71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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galaxyp
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71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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245 </scan>
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246 </scanList>
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galaxyp
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galaxyp
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galaxyp
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galaxyp
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galaxyp
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galaxyp
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71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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60ee8c592b13 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
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60ee8c592b13 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
galaxyp
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71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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261 </binaryDataArray>
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262 </binaryDataArrayList>
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71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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271 <scan>
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71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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275 </scanList>
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282 <binary/>
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283 </binaryDataArray>
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284 <binaryDataArray encodedLength="0">
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60ee8c592b13 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
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71411ac28268 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
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290 </binaryDataArray>
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291 </binaryDataArrayList>
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292 </spectrum>
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300 <scan>
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304 </scanList>
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312 </binaryDataArray>
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313 <binaryDataArray encodedLength="0">
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60ee8c592b13 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
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319 </binaryDataArray>
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