Mercurial > repos > galaxyp > cardinal_preprocessing
view test-data/out4.imzml @ 5:ed9ed1e6cca2 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
author | galaxyp |
---|---|
date | Fri, 13 Dec 2019 13:57:13 -0500 |
parents | 1b875f0b8024 |
children | 5bf056c0354e |
line wrap: on
line source
<?xml version="1.0"?> <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"> <cvList count="3"> <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" /> <cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" /> <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" /> </cvList> <fileDescription> <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{2567A8C4-D2AF-4C81-874C-82E9134A080C}" /> <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="EA722C9CF5A229ACF6AEAD177908D73A1C8CB44E" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> <referenceableParamGroupList count="4"> <referenceableParamGroup id="spectrum1"> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> </referenceableParamGroup> <referenceableParamGroup id="scan1"> <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" /> <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" /> </referenceableParamGroup> <referenceableParamGroup id="mzArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> </referenceableParamGroup> <referenceableParamGroup id="intensityArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> </referenceableParamGroup> </referenceableParamGroupList> <sampleList count="1"> <sample id="sample1" name="Sample1"> <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" /> </sample> </sampleList> <softwareList count="1"> <software id="Cardinal" version="1.12.1"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> <scanSettingsList count="1"> <scanSettings id="scansettings1"> <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" /> </scanSettings> </scanSettingsList> <instrumentConfigurationList count="1"> <instrumentConfiguration id="IC1" /> </instrumentConfigurationList> <dataProcessingList count="1"> <dataProcessing id="CardinalWriteImzML"> <processingMethod order="1" softwareRef="Cardinal"> <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" /> </processingMethod> </dataProcessing> </dataProcessingList> <run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1"> <spectrumList count="5" defaultDataProcessingRef="CardinalWriteImzML"> <spectrum id="Spectrum=1" defaultArrayLength="0" index="1"> <referenceableParamGroupRef ref="spectrum1" /> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> <scan instrumentConfigurationRef="IC1"> <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4812" /> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Spectrum=2" defaultArrayLength="0" index="2"> <referenceableParamGroupRef ref="spectrum1" /> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> <scan instrumentConfigurationRef="IC1"> <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="9608" /> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Spectrum=3" defaultArrayLength="0" index="3"> <referenceableParamGroupRef ref="spectrum1" /> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> <scan instrumentConfigurationRef="IC1"> <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="14404" /> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Spectrum=4" defaultArrayLength="0" index="4"> <referenceableParamGroupRef ref="spectrum1" /> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> <scan instrumentConfigurationRef="IC1"> <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="19200" /> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Spectrum=5" defaultArrayLength="0" index="5"> <referenceableParamGroupRef ref="spectrum1" /> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" /> <scan instrumentConfigurationRef="IC1"> <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="23996" /> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" /> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" /> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> </spectrumList> </run> </mzML>