Mercurial > repos > galaxyp > maldi_quant_peak_detection

annotate test-data/peak_detection4.imzml @ 4:e9300ef37403 draft

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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 160538a890a6
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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="{a9ea11c4-975e-4f4a-a174-906e8cf0bb77}"/>
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12 <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7022792264dc3f66251f22bebb634de68cb6a9fc"/>
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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 </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="13"/>
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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="1300" 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="24" defaultDataProcessingRef="export">
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56 <spectrum index="0" id="scan=0" defaultArrayLength="90">
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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="900.470520019531" 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="999.455810546875" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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61 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
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62 <scanList count="1">
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63 <scan>
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64 <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
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65 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
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66 </scan>
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67 </scanList>
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68 <binaryDataArrayList count="2">
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69 <binaryDataArray encodedLength="0">
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70 <referenceableParamGroupRef ref="mzArray"/>
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71 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
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72 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="90"/>
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73 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="720"/>
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74 <binary/>
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75 </binaryDataArray>
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76 <binaryDataArray encodedLength="0">
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77 <referenceableParamGroupRef ref="intensityArray"/>
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732 <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
733 </scan>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
734 </scanList>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
735 <binaryDataArrayList count="2">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
736 <binaryDataArray encodedLength="0">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
737 <referenceableParamGroupRef ref="mzArray"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
738 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="28752"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
739 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="65"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
740 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="520"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
741 <binary/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
742 </binaryDataArray>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
743 <binaryDataArray encodedLength="0">
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
744 <referenceableParamGroupRef ref="intensityArray"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
745 <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="29272"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
746 <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="65"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
747 <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="520"/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
748 <binary/>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
749 </binaryDataArray>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
750 </binaryDataArrayList>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
751 </spectrum>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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diff changeset
752 </spectrumList>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
diff changeset
753 </run>
36d38d2cf88c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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754 </mzML>