annotate test-data/preprocessing_results1.imzml @ 2:cbc7e53518ce draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1

<?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:1000127" name="centroid spectrum" value="" />
			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{002DF5BA-0549-44DF-A8BB-27DA3E197EB7}" />
			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0379019A6F9D0B55F9217420030633F7163AF9D3" />
			<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:1000127" name="centroid 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="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="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<binary />
					</binaryDataArray>
					<binaryDataArray encodedLength="0">
						<referenceableParamGroupRef ref="intensityArray" />
						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="24" />
						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<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="2" />
						<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="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<binary />
					</binaryDataArray>
					<binaryDataArray encodedLength="0">
						<referenceableParamGroupRef ref="intensityArray" />
						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="32" />
						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<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="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="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<binary />
					</binaryDataArray>
					<binaryDataArray encodedLength="0">
						<referenceableParamGroupRef ref="intensityArray" />
						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="40" />
						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<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="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="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<binary />
					</binaryDataArray>
					<binaryDataArray encodedLength="0">
						<referenceableParamGroupRef ref="intensityArray" />
						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="48" />
						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<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="2" />
						<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="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<binary />
					</binaryDataArray>
					<binaryDataArray encodedLength="0">
						<referenceableParamGroupRef ref="intensityArray" />
						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="56" />
						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<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="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="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<binary />
					</binaryDataArray>
					<binaryDataArray encodedLength="0">
						<referenceableParamGroupRef ref="intensityArray" />
						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="64" />
						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<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="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="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<binary />
					</binaryDataArray>
					<binaryDataArray encodedLength="0">
						<referenceableParamGroupRef ref="intensityArray" />
						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="72" />
						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<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="2" />
						<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="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<binary />
					</binaryDataArray>
					<binaryDataArray encodedLength="0">
						<referenceableParamGroupRef ref="intensityArray" />
						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="80" />
						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<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="3" />
						<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="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<binary />
					</binaryDataArray>
					<binaryDataArray encodedLength="0">
						<referenceableParamGroupRef ref="intensityArray" />
						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="88" />
						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />
						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />
						<binary />
					</binaryDataArray>
				</binaryDataArrayList>
			</spectrum>
		</spectrumList>
	</run>
</mzML>