Mercurial > repos > galaxyp > cardinal_quality_report

diff test-data/preprocessing_results1.imzml @ 7:74b61bf5bc4b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
author galaxyp
date Wed, 25 Mar 2020 06:02:50 -0400
parents 16556ca0196b
children 0d4d4f16d455
line wrap: on
line diff
--- a/test-data/preprocessing_results1.imzml	Fri Dec 13 13:53:41 2019 -0500
+++ b/test-data/preprocessing_results1.imzml	Wed Mar 25 06:02:50 2020 -0400
@@ -9,8 +9,8 @@
 		<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="{728FBFFE-E6FC-4283-8068-393A66F6BD5C}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="375094460F3B80674CB2F541DCD9928B3D61B2FF" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="722d404b-4188-40b4-a3b2-3764ebbdecad" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c5aded0bab57fd7317901ff7709f2395fc91152e" />
 			<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">
@@ -43,7 +42,7 @@
 		</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>
@@ -51,10 +50,16 @@
 		<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="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">
@@ -73,21 +78,23 @@
 						<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">
 					<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -100,21 +107,23 @@
 						<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" />
+						<userParam name="3DPositionX" value="2.000000" />
+						<userParam name="3DPositionY" value="1.000000" />
 					</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" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="56" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -127,21 +136,23 @@
 						<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">
 					<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="76" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -154,21 +165,23 @@
 						<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">
 					<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="96" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -181,21 +194,23 @@
 						<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">
 					<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="116" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -208,21 +223,23 @@
 						<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">
 					<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="136" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -235,21 +252,23 @@
 						<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">
 					<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="156" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -262,21 +281,23 @@
 						<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">
 					<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="176" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -289,21 +310,23 @@
 						<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">
 					<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="196" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>