Mercurial > repos > galaxyp > cardinal_spectra_plots

diff test-data/out5.imzml @ 6:043f9c91f686 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
author galaxyp
date Wed, 25 Mar 2020 05:53:20 -0400
parents 3642ed221eb2
children 0b7e00e5b9d2
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line diff
--- a/test-data/out5.imzml	Fri Dec 13 13:52:57 2019 -0500
+++ b/test-data/out5.imzml	Wed Mar 25 05:53:20 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="{CC0B2B92-FB40-42C8-822F-834AA528954C}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0B644915E88274BE83FBB110D4CC6D0CDFABAAAC" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="87b0ab73-abe6-4eb6-91ba-b6d493a343bc" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9de3a02d0943ecda0717845511a8f7b8f58d1db7" />
 			<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:1000043" name="max count of pixel y" value="3" />
+			<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="2" />
+			<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="1.000000" />
+			<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="2" />
+						<userParam name="3DPositionX" value="1.000000" />
+						<userParam name="3DPositionY" value="2.000000" />
 					</scan>
 				</scanList>
 				<binaryDataArrayList count="2">
@@ -100,6 +107,8 @@
 						<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" />
+						<userParam name="3DPositionX" value="2.000000" />
+						<userParam name="3DPositionY" value="2.000000" />
 					</scan>
 				</scanList>
 				<binaryDataArrayList count="2">
@@ -127,6 +136,8 @@
 						<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">
@@ -154,6 +165,8 @@
 						<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">
@@ -181,6 +194,8 @@
 						<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" />
+						<userParam name="3DPositionX" value="2.000000" />
+						<userParam name="3DPositionY" value="3.000000" />
 					</scan>
 				</scanList>
 				<binaryDataArrayList count="2">
@@ -208,6 +223,8 @@
 						<referenceableParamGroupRef ref="scan1" />
 						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
 						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+						<userParam name="3DPositionX" value="3.000000" />
+						<userParam name="3DPositionY" value="3.000000" />
 					</scan>
 				</scanList>
 				<binaryDataArrayList count="2">