changeset 5:ed9ed1e6cca2 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
author galaxyp
date Fri, 13 Dec 2019 13:57:13 -0500
parents 141a9288be9c
children 5bf056c0354e
files preprocessing.xml test-data/112_annotation_output.tabular test-data/112_auto_combined.ibd test-data/112_auto_combined.imzml test-data/112_auto_combined.imzml.txt test-data/112_auto_combined_QC.pdf test-data/123_annotation_output.tabular test-data/123_combine.rdata test-data/123_combined.RData test-data/123_combined.ibd test-data/123_combined.imzml test-data/123_combined.imzml.txt test-data/123_combined_QC.pdf test-data/123_combined_auto.ibd test-data/123_combined_auto.imzml test-data/123_combined_auto.imzml.txt test-data/123_combined_auto.pdf test-data/123_combined_picked.rdata test-data/123_combined_picked2.rdata test-data/12_annotation_output.tabular test-data/12_combined.RData test-data/12_combined.ibd test-data/12_combined.imzml test-data/12_combined.imzml.txt test-data/12_combined_QC.pdf test-data/2123_auto_combined.RData test-data/2123_auto_combined.ibd test-data/2123_auto_combined.imzml test-data/2123_auto_combined.imzml.txt test-data/2123_auto_combined_QC.pdf test-data/picked.ibd test-data/picked.imzml test-data/picked.imzml.txt test-data/picked.tabular test-data/picked_QC.pdf test-data/xy_coordinates2.tabular
diffstat 36 files changed, 1967 insertions(+), 62 deletions(-) [+]
line wrap: on
line diff
--- a/preprocessing.xml	Fri Mar 22 08:12:42 2019 -0400
+++ b/preprocessing.xml	Fri Dec 13 13:57:13 2019 -0500
@@ -494,7 +494,7 @@
                             <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/>
                         </when>
                         <when value="align_msidata_ref">
-                            <param name="align_peaks_msidata" type="data" format="rdata," label="Picked and aligned Cardinal MSImageSet saved as RData"/>
+                            <param name="align_peaks_msidata" type="data" format="rdata" label="Picked and aligned Cardinal MSImageSet saved as RData"/>
                         </when>
                     </conditional>
                 </when>
@@ -543,7 +543,7 @@
                                     <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to extract from input file"/>
                                 </when>
                                 <when value="msidata_ref">
-                                    <param name="peaks_msidata" type="data" format="rdata," label="Picked and aligned Cardinal MSImageSet saved as RData"/>
+                                    <param name="peaks_msidata" type="data" format="rdata" label="Picked and aligned Cardinal MSImageSet saved as RData"/>
                                 </when>
                             </conditional>
                         </when>
--- a/test-data/112_annotation_output.tabular	Fri Mar 22 08:12:42 2019 -0400
+++ b/test-data/112_annotation_output.tabular	Fri Dec 13 13:57:13 2019 -0500
@@ -1,16 +1,16 @@
-x	y	sample_name	file_name	column_name	NA.x	NA.y	NA
-1	1	msidata_1.RData	file_one	col1	NA	NA	NA
-1	2	msidata_1.RData	file_one	col1	NA	NA	NA
-1	3	msidata_1.RData	file_one	col1	NA	NA	NA
-10	1	123_combined.RData	file_two	col3	NA	NA	NA
-10	2	123_combined.RData	file_two	col3	NA	NA	NA
-10	3	123_combined.RData	file_two	col3	NA	NA	NA
-15	1	123_combined.RData	file_three	col3	NA	NA	NA
-15	2	123_combined.RData	file_three	col3	NA	NA	NA
-15	3	123_combined.RData	file_three	col3	NA	NA	NA
-7	1	123_combined.RData	file_one	col1	NA	NA	NA
-7	2	123_combined.RData	file_one	col1	NA	NA	NA
-7	3	123_combined.RData	file_one	col1	NA	NA	NA
-9	1	123_combined.RData	file_two	col2	NA	NA	NA
-9	2	123_combined.RData	file_two	col2	NA	NA	NA
-9	3	123_combined.RData	file_two	col2	NA	NA	NA
+x	y	sample_name	file_name	column_name
+1	1	msidata_1.RData	file_one	col1
+1	2	msidata_1.RData	file_one	col1
+1	3	msidata_1.RData	file_one	col1
+7	1	123_combined.RData	file_one	col1
+7	2	123_combined.RData	file_one	col1
+7	3	123_combined.RData	file_one	col1
+9	1	123_combined.RData	file_two	col2
+10	1	123_combined.RData	file_two	col3
+9	2	123_combined.RData	file_two	col2
+10	2	123_combined.RData	file_two	col3
+9	3	123_combined.RData	file_two	col2
+10	3	123_combined.RData	file_two	col3
+15	1	123_combined.RData	file_three	col3
+15	2	123_combined.RData	file_three	col3
+15	3	123_combined.RData	file_three	col3
Binary file test-data/112_auto_combined.ibd has changed
--- a/test-data/112_auto_combined.imzml	Fri Mar 22 08:12:42 2019 -0400
+++ b/test-data/112_auto_combined.imzml	Fri Dec 13 13:57:13 2019 -0500
@@ -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="{00A83E55-A8F8-41D4-BBAC-345FA77AAB7E}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9B17E43E3D3B35BE3CD0AE65F40E0C6B27C2752F" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="a0620366-fee2-4a2a-a643-0f0e0c9ae5a6" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9bcd78ace1e6441dc527501b5eb3994fcf15b894" />
 			<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="2.2.6">
 			<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="15" />
+			<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="5" />
 			<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="15" />
+			<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">
--- a/test-data/112_auto_combined.imzml.txt	Fri Mar 22 08:12:42 2019 -0400
+++ b/test-data/112_auto_combined.imzml.txt	Fri Dec 13 13:57:13 2019 -0500
@@ -1,4 +1,4 @@
 imzML file:
 total 556
--rw-r--r-- 1 meli meli 537552 Feb 12 12:25 ibd
--rw-r--r-- 1 meli meli  25466 Feb 12 12:25 imzml
+-rw-r--r-- 1 meli meli 537552 Dez 11 00:10 ibd
+-rw-r--r-- 1 meli meli  25811 Dez 11 00:10 imzml
Binary file test-data/112_auto_combined_QC.pdf has changed
--- a/test-data/123_annotation_output.tabular	Fri Mar 22 08:12:42 2019 -0400
+++ b/test-data/123_annotation_output.tabular	Fri Dec 13 13:57:13 2019 -0500
@@ -1,13 +1,13 @@
-x	y	sample_name	file_name	column_name	NA.x	NA.y	NA
-1	1	File1	file_one	col1	NA	NA	NA
-1	2	File1	file_one	col1	NA	NA	NA
-1	3	File1	file_one	col1	NA	NA	NA
-3	1	File2	file_two	col2	NA	NA	NA
-3	2	File2	file_two	col2	NA	NA	NA
-3	3	File2	file_two	col2	NA	NA	NA
-4	1	File2	file_two	col3	NA	NA	NA
-4	2	File2	file_two	col3	NA	NA	NA
-4	3	File2	file_two	col3	NA	NA	NA
-9	1	File3	file_three	col3	NA	NA	NA
-9	2	File3	file_three	col3	NA	NA	NA
-9	3	File3	file_three	col3	NA	NA	NA
+x	y	sample_name	file_name	column_name
+1	1	File1	file_one	col1
+1	2	File1	file_one	col1
+1	3	File1	file_one	col1
+3	1	File2	file_two	col2
+4	1	File2	file_two	col3
+3	2	File2	file_two	col2
+4	2	File2	file_two	col3
+3	3	File2	file_two	col2
+4	3	File2	file_two	col3
+9	1	File3	file_three	col3
+9	2	File3	file_three	col3
+9	3	File3	file_three	col3
Binary file test-data/123_combine.rdata has changed
Binary file test-data/123_combined.RData has changed
Binary file test-data/123_combined.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined.imzml	Fri Dec 13 13:57:13 2019 -0500
@@ -0,0 +1,399 @@
+<?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:1000128" name="profile spectrum" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="8421b4d5-42be-4040-9d94-0398a40d6121" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d2cf2df8db9b95afd23834703bc933df1098bb6d" />
+			<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:1000128" name="profile spectrum" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="scan1">
+			<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" 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="" />
+		</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>
+	</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="2.2.6">
+			<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="4" />
+			<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="9" />
+			<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" />
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+	</scanSettingsList>
+	<instrumentConfigurationList count="1">
+		<instrumentConfiguration id="IC1">
+			<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+		</instrumentConfiguration>
+	</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="12" 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">
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+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
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+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
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+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
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+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
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+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
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+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
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+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
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+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
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+				<referenceableParamGroupRef ref="spectrum1" />
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+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
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+					<binaryDataArray encodedLength="0">
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+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
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+				<referenceableParamGroupRef ref="spectrum1" />
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+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
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+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
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+				<referenceableParamGroupRef ref="spectrum1" />
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+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
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+				<referenceableParamGroupRef ref="spectrum1" />
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+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
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+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
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+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380" />
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=10" defaultArrayLength="0" index="10">
+				<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="9" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
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+						<binary />
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<binary />
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+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
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+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+					</scan>
+				</scanList>
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+						<referenceableParamGroupRef ref="mzArray" />
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+						<binary />
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+					<binaryDataArray encodedLength="0">
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=12" defaultArrayLength="0" index="12">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
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+						<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="8399" />
+						<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:1000102" name="external offset" value="403168" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+		</spectrumList>
+	</run>
+</mzML>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined.imzml.txt	Fri Dec 13 13:57:13 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 452
+-rw-r--r-- 1 meli meli 436764 Dez 11 00:02 ibd
+-rw-r--r-- 1 meli meli  21511 Dez 11 00:02 imzml
Binary file test-data/123_combined_QC.pdf has changed
Binary file test-data/123_combined_auto.ibd has changed
--- a/test-data/123_combined_auto.imzml	Fri Mar 22 08:12:42 2019 -0400
+++ b/test-data/123_combined_auto.imzml	Fri Dec 13 13:57:13 2019 -0500
@@ -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="{7DC9B0BB-277B-4A92-8780-2879E0E6A8F2}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="6768CFB740661C3F0C560438B85A906EA05933D5" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c12d4d26-5ff1-4c3c-99ea-95e0858faf36" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="147d6aa7f71a366246c93d750fcc9240b84c748f" />
 			<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="" />
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 			<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="2.2.6">
 			<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="8" />
-			<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="11" />
+			<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="6" />
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+			<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">
--- a/test-data/123_combined_auto.imzml.txt	Fri Mar 22 08:12:42 2019 -0400
+++ b/test-data/123_combined_auto.imzml.txt	Fri Dec 13 13:57:13 2019 -0500
@@ -1,4 +1,4 @@
 imzML file:
 total 452
--rw-r--r-- 1 meli meli 436764 Feb 12 00:51 ibd
--rw-r--r-- 1 meli meli  21166 Feb 12 00:51 imzml
+-rw-r--r-- 1 meli meli 436764 Dez 11 00:05 ibd
+-rw-r--r-- 1 meli meli  21514 Dez 11 00:05 imzml
Binary file test-data/123_combined_auto.pdf has changed
Binary file test-data/123_combined_picked.rdata has changed
Binary file test-data/123_combined_picked2.rdata has changed
--- a/test-data/12_annotation_output.tabular	Fri Mar 22 08:12:42 2019 -0400
+++ b/test-data/12_annotation_output.tabular	Fri Dec 13 13:57:13 2019 -0500
@@ -1,10 +1,10 @@
-x	y	sample_name	file_name	column_name	NA.x	NA.y	NA
-1	1	msidata_1.RData	file_one	col1	NA	NA	NA
-1	2	msidata_1.RData	file_one	col1	NA	NA	NA
-1	3	msidata_1.RData	file_one	col1	NA	NA	NA
-7	1	msidata_2.RData	file_two	col2	NA	NA	NA
-7	2	msidata_2.RData	file_two	col2	NA	NA	NA
-7	3	msidata_2.RData	file_two	col2	NA	NA	NA
-8	1	msidata_2.RData	file_two	col3	NA	NA	NA
-8	2	msidata_2.RData	file_two	col3	NA	NA	NA
-8	3	msidata_2.RData	file_two	col3	NA	NA	NA
+x	y	sample_name	file_name	column_name
+1	1	msidata_1.RData	file_one	col1
+1	2	msidata_1.RData	file_one	col1
+1	3	msidata_1.RData	file_one	col1
+7	1	msidata_2.RData	file_two	col2
+8	1	msidata_2.RData	file_two	col3
+7	2	msidata_2.RData	file_two	col2
+8	2	msidata_2.RData	file_two	col3
+7	3	msidata_2.RData	file_two	col2
+8	3	msidata_2.RData	file_two	col3
Binary file test-data/12_combined.RData has changed
Binary file test-data/12_combined.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/12_combined.imzml	Fri Dec 13 13:57:13 2019 -0500
@@ -0,0 +1,318 @@
+<?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:1000128" name="profile spectrum" value="" />
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+			<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:1000128" name="profile spectrum" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="scan1">
+			<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="mzArray">
+			<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
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+			<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="" />
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+			<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
+			<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
+		</referenceableParamGroup>
+	</referenceableParamGroupList>
+	<sampleList count="1">
+		<sample id="sample1" name="Sample1">
+			<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />
+		</sample>
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+		</software>
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/12_combined.imzml.txt	Fri Dec 13 13:57:13 2019 -0500
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+imzML file:
+total 352
+-rw-r--r-- 1 meli meli 335976 Dez 11 00:07 ibd
+-rw-r--r-- 1 meli meli  17217 Dez 11 00:07 imzml
Binary file test-data/12_combined_QC.pdf has changed
Binary file test-data/2123_auto_combined.RData has changed
Binary file test-data/2123_auto_combined.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2123_auto_combined.imzml	Fri Dec 13 13:57:13 2019 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2123_auto_combined.imzml.txt	Fri Dec 13 13:57:13 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 656
+-rw-r--r-- 1 meli meli 638340 Dez 11 00:12 ibd
+-rw-r--r-- 1 meli meli  30107 Dez 11 00:12 imzml
Binary file test-data/2123_auto_combined_QC.pdf has changed
Binary file test-data/picked.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picked.imzml	Fri Dec 13 13:57:13 2019 -0500
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+      <binary/>
+     </binaryDataArray>
+    </binaryDataArrayList>
+   </spectrum>
+  </spectrumList>
+ </run>
+</mzML>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picked.imzml.txt	Fri Dec 13 13:57:13 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 192
+-rw-r--r-- 1 meli meli 157984 Dez 11 00:03 ibd
+-rw-r--r-- 1 meli meli  35012 Dez 11 00:03 imzml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picked.tabular	Fri Dec 13 13:57:13 2019 -0500
@@ -0,0 +1,19 @@
+x	y	sample_name
+1	1	File1
+1	2	File1
+1	3	File1
+3	1	File1
+4	1	File1
+3	2	File1
+4	2	File1
+3	3	File1
+4	3	File1
+11	1	File2
+12	1	File2
+11	2	File2
+12	2	File2
+11	3	File2
+12	3	File2
+17	1	File2
+17	2	File2
+17	3	File2
Binary file test-data/picked_QC.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xy_coordinates2.tabular	Fri Dec 13 13:57:13 2019 -0500
@@ -0,0 +1,2 @@
+0	0	File1
+8	0	File2