Mercurial > repos > galaxyp > mass_spectrometry_imaging_segmentations
diff test-data/Example_Continuous.imzML @ 0:0c1a9b68f436 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b
author | galaxyp |
---|---|
date | Sat, 24 Feb 2018 13:51:32 -0500 |
parents | |
children | cee9cf693709 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Example_Continuous.imzML Sat Feb 24 13:51:32 2018 -0500 @@ -0,0 +1,373 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<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_idx.xsd" version="1.1"> + <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="{554A27FA-79D2-4766-9A2C-862E6D78B1F3}"/> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="A5BE532D25997B71BE6D20C76561DDC4D5307DDD"/> + <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value=""/> + </fileContent> + <sourceFileList count="1"> + <sourceFile id="sf1" name="Example.raw" location="C:\Users\Thorsten Schramm\Documents\Promotion\imzML\Website\files\Beispiel-Dateien\Example images\"> + <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW file" value=""/> + <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/> + <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/> + </sourceFile> + </sourceFileList> + <contact> + <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/> + <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institut für Anorganische und Analytische Chemie"/> + <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstraße 60, Haus 16, Gießen, Germany"/> + <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/> + </contact> + </fileDescription> + <referenceableParamGroupList count="4"> + <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> + <referenceableParamGroup id="scan1"> + <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value=""/> + <cvParam cvRef="MS" accession="MS:1000095" name="linear" value=""/> + <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/> + </referenceableParamGroup> + <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=""/> + <cvParam cvRef="MS" accession="MS:1000129" name="negative scan" 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="2"> + <software id="Xcalibur" version="2.2"> + <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/> + </software> + <software id="TMC" version="1.1 beta"> + <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:1000401" name="top down" value=""/> + <cvParam cvRef="IMS" accession="IMS:1000413" name="flyback" value=""/> + <cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan" value=""/> + <cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right" value=""/> + <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="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/> + <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/> + <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/> + <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/> + <cvParam cvRef="MS" accession="MS:1000836" name="dried dropplet" value=""/> + <cvParam cvRef="MS" accession="MS:1000835" name="matrix solution concentration" value="10"/> + <cvParam cvRef="MS" accession="MS:1000834" name="matrix solution" value="DHB"/> + </scanSettings> + </scanSettingsList> + <instrumentConfigurationList count="1"> + <instrumentConfiguration id="LTQFTUltra0"> + <cvParam cvRef="MS" accession="MS:1000557" name="LTQ FT Ultra" value=""/> + <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="none"/> + <componentList count="3"> + <source order="1"> + <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/> + <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/> + <cvParam cvRef="MS" accession="MS:1000843" name="wavelength" value="337"/> + <cvParam cvRef="MS" accession="MS:1000844" name="focus diameter x" value="10"/> + <cvParam cvRef="MS" accession="MS:1000845" name="focus diameter y" value="10"/> + <cvParam cvRef="MS" accession="MS:1000846" name="pulse energy" value="10"/> + <cvParam cvRef="MS" accession="MS:1000847" name="pulse duration" value="10"/> + <cvParam cvRef="MS" accession="MS:1000848" name="attenuation" value="50"/> + <cvParam cvRef="MS" accession="MS:1000850" name="gas laser" value=""/> + <cvParam cvRef="IMS" accession="IMS:1000202" name="target material" value="Conductive Glas"/> + </source> + <analyzer order="2"> + <cvParam cvRef="MS" accession="MS:1000264" name="ion trap" value=""/> + <cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + </analyzer> + <detector order="3"> + <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/> + <cvParam cvRef="MS" accession="MS:1000120" name="transient recorder" value=""/> + </detector> + </componentList> + <softwareRef ref="Xcalibur"/> + </instrumentConfiguration> + </instrumentConfigurationList> + <dataProcessingList count="2"> + <dataProcessing id="XcaliburProcessing"> + <processingMethod order="1" softwareRef="Xcalibur"> + <cvParam cvRef="MS" accession="MS:1000594" name="low intensity data point removal" value=""/> + </processingMethod> + </dataProcessing> + <dataProcessing id="TMCConversion"> + <processingMethod order="2" softwareRef="TMC"> + <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> + </processingMethod> + </dataProcessing> + </dataProcessingList> + <run defaultInstrumentConfigurationRef="LTQFTUltra0" defaultSourceFileRef="sf1" id="Experiment01" sampleRef="sample1" startTimeStamp="2009-08-11T15:59:44"> + <spectrumList count="9" defaultDataProcessingRef="XcaliburProcessing"> + <spectrum id="Scan=1" defaultArrayLength="0" index="0"> + <referenceableParamGroupRef ref="spectrum1"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan instrumentConfigurationRef="LTQFTUltra0"> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33612"/> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> + <binary/> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Scan=2" defaultArrayLength="0" index="1"> + <referenceableParamGroupRef ref="spectrum1"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan instrumentConfigurationRef="LTQFTUltra0"> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208"/> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> + <binary/> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Scan=3" defaultArrayLength="0" index="2"> + <referenceableParamGroupRef ref="spectrum1"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan instrumentConfigurationRef="LTQFTUltra0"> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100804"/> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> + <binary/> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Scan=4" defaultArrayLength="0" index="3"> + <referenceableParamGroupRef ref="spectrum1"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan instrumentConfigurationRef="LTQFTUltra0"> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400"/> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> + <binary/> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Scan=5" defaultArrayLength="0" index="4"> + <referenceableParamGroupRef ref="spectrum1"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan instrumentConfigurationRef="LTQFTUltra0"> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996"/> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> + <binary/> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Scan=6" defaultArrayLength="0" index="5"> + <referenceableParamGroupRef ref="spectrum1"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan instrumentConfigurationRef="LTQFTUltra0"> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592"/> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> + <binary/> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Scan=7" defaultArrayLength="0" index="6"> + <referenceableParamGroupRef ref="spectrum1"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan instrumentConfigurationRef="LTQFTUltra0"> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188"/> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> + <binary/> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Scan=8" defaultArrayLength="0" index="7"> + <referenceableParamGroupRef ref="spectrum1"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan instrumentConfigurationRef="LTQFTUltra0"> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="268784"/> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> + <binary/> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum id="Scan=9" defaultArrayLength="0" index="8"> + <referenceableParamGroupRef ref="spectrum1"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan instrumentConfigurationRef="LTQFTUltra0"> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/> + <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:1000103" name="external array length" value="8399"/> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380"/> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> + <binary/> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + </spectrumList> + </run> +</mzML> \ No newline at end of file