Mercurial > repos > galaxyp > cardinal_preprocessing
diff test-data/out4.imzml @ 6:5bf056c0354e draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
| author | galaxyp |
|---|---|
| date | Wed, 25 Mar 2020 08:13:17 -0400 |
| parents | 1b875f0b8024 |
| children | ca727a6dede6 |
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--- a/test-data/out4.imzml Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/out4.imzml Wed Mar 25 08:13:17 2020 -0400 @@ -9,8 +9,8 @@ <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:1000080" name="universally unique identifier" value="b0dec95e-b66f-4c3f-86df-166d942f42c3" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d9b557cf2c0e15a0cdd863e50897b07a55a26f31" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -22,19 +22,18 @@ </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" /> + <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="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> </referenceableParamGroupList> <sampleList count="1"> @@ -43,18 +42,24 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="1.12.1"> + <software id="Cardinal" version="2.4.0"> <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:1000042" name="max count of pixel x" value="2" /> <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="3" /> + <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="2.000000" /> + <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" /> </scanSettings> </scanSettingsList> <instrumentConfigurationList count="1"> - <instrumentConfiguration id="IC1" /> + <instrumentConfiguration id="IC1"> + <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" /> + </instrumentConfiguration> </instrumentConfigurationList> <dataProcessingList count="1"> <dataProcessing id="CardinalWriteImzML"> @@ -73,6 +78,8 @@ <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" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -100,6 +107,8 @@ <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" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -127,6 +136,8 @@ <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" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -154,6 +165,8 @@ <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" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -181,6 +194,8 @@ <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" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2">