Mercurial > repos > galaxyp > cardinal_quality_report
diff test-data/12_combined.imzml @ 6:19f68d9ae773 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
| author | galaxyp |
|---|---|
| date | Fri, 13 Dec 2019 13:53:41 -0500 |
| parents | |
| children | bb9500286fe4 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12_combined.imzml Fri Dec 13 13:53:41 2019 -0500 @@ -0,0 +1,318 @@ +<?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="e9aca5c3-32c8-416b-a9e9-e40ba239ce32" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c0c53177dc3a008c7a18ba10fe139ccaecc295a2" /> + <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="" /> + </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="" /> + </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="" /> + </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="2.2.6"> + <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" /> + <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="8" /> + <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" /> + <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" /> + </scanSettings> + </scanSettingsList> + <instrumentConfigurationList count="1"> + <instrumentConfiguration id="IC1"> + <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" /> + </instrumentConfiguration> + </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="9" 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="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + <binaryDataArray encodedLength="0"> + <referenceableParamGroupRef ref="intensityArray" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33612" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <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="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="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + <binaryDataArray encodedLength="0"> + <referenceableParamGroupRef ref="intensityArray" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <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="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="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + <binaryDataArray encodedLength="0"> + <referenceableParamGroupRef ref="intensityArray" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100804" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <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="7" /> + <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="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + <binaryDataArray encodedLength="0"> + <referenceableParamGroupRef ref="intensityArray" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <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="8" /> + <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="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + <binaryDataArray encodedLength="0"> + <referenceableParamGroupRef ref="intensityArray" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Spectrum=6" defaultArrayLength="0" index="6"> + <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="7" /> + <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="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + <binaryDataArray encodedLength="0"> + <referenceableParamGroupRef ref="intensityArray" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Spectrum=7" defaultArrayLength="0" index="7"> + <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="8" /> + <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="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + <binaryDataArray encodedLength="0"> + <referenceableParamGroupRef ref="intensityArray" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Spectrum=8" defaultArrayLength="0" index="8"> + <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="7" /> + <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="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + <binaryDataArray encodedLength="0"> + <referenceableParamGroupRef ref="intensityArray" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="268784" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Spectrum=9" defaultArrayLength="0" index="9"> + <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="8" /> + <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="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + <binaryDataArray encodedLength="0"> + <referenceableParamGroupRef ref="intensityArray" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" /> + <binary /> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + </spectrumList> + </run> +</mzML>