Mercurial > repos > galaxyp > cardinal_segmentations

changeset 12:050bcc806da2 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
author galaxyp
date Sun, 29 Nov 2020 23:37:41 +0000
parents 0159b15b1281
children cc430977c8ff
files segmentation.xml test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_processed.pdf test-data/Heatmaps_rdata.pdf test-data/centroids_proc.pdf test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results1.pdf test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results2.pdf test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results3.pdf
diffstat 19 files changed, 118 insertions(+), 121 deletions(-) [+]
line wrap: on
line diff
--- a/segmentation.xml	Tue Oct 06 08:04:35 2020 +0000
+++ b/segmentation.xml	Sun Nov 29 23:37:41 2020 +0000
@@ -381,14 +381,11 @@
             <output name="pixeloutput" file="classes_ssc.tabular"/>
         </test>
         <test>
-            <param name="infile" value="" ftype="imzml">
-                <composite_data value="preprocessing_results3.imzml"/>
-                <composite_data value="preprocessing_results3.ibd"/>
-            </param>
+           <expand macro="processed_infile_imzml"/>
             <conditional name="processed_cond">
                 <param name="processed_file" value="processed"/>
-                <param name="accuracy" value="1"/>
-                <param name="units" value="mz"/>
+                <param name="accuracy" value="200"/>
+                <param name="units" value="ppm"/>
             </conditional>
             <param name="segmentationtool" value="centroids"/>
             <param name="centroids_r" value="1"/>
@@ -408,10 +405,10 @@
             <output name="pixeloutput" file="classes_proc.tabular"/>
             <output name="mzfeatures">
                 <assert_contents>
-                    <has_text text="1212" />
-                    <has_text text="1297" />
-                    <has_text text="1199" />
-                    <has_text text="1298" />
+                    <has_text text="100.642" />
+                    <has_text text="101.816297645089" />
+                    <has_text text="1.34687866193417" />
+                    <has_text text="6.43855724908388" />
                     <has_n_columns n="9" />
                     <has_n_lines n="101" />
                 </assert_contents>
Binary file test-data/Heatmaps_LM8_file16.pdf has changed
Binary file test-data/Heatmaps_analyze75.pdf has changed
Binary file test-data/Heatmaps_imzml.pdf has changed
Binary file test-data/Heatmaps_processed.pdf has changed
Binary file test-data/Heatmaps_rdata.pdf has changed
Binary file test-data/centroids_proc.pdf has changed
Binary file test-data/preprocessing_results1.ibd has changed
--- a/test-data/preprocessing_results1.imzml	Tue Oct 06 08:04:35 2020 +0000
+++ b/test-data/preprocessing_results1.imzml	Sun Nov 29 23:37:41 2020 +0000
@@ -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="" />
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@@ -86,15 +86,15 @@
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
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+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
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@@ -115,15 +115,15 @@
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+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
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@@ -144,15 +144,15 @@
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
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+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
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@@ -173,15 +173,15 @@
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
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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="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="144" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
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@@ -202,15 +202,15 @@
 					<binaryDataArray encodedLength="0">
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
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+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
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@@ -231,15 +231,15 @@
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
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 					<binaryDataArray encodedLength="0">
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="208" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
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@@ -260,15 +260,15 @@
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
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-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="240" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
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@@ -289,15 +289,15 @@
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
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-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="272" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
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@@ -318,15 +318,15 @@
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="304" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
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--- a/test-data/preprocessing_results1.imzml.txt	Tue Oct 06 08:04:35 2020 +0000
+++ b/test-data/preprocessing_results1.imzml.txt	Sun Nov 29 23:37:41 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-rw-r-- 1 meli meli   216 Oct  5 19:57 ibd
--rw-rw-r-- 1 meli meli 18090 Oct  5 19:57 imzml
+-rw-rw-r-- 1 meli meli   336 Nov 29 01:14 ibd
+-rw-rw-r-- 1 meli meli 18092 Nov 29 01:14 imzml
Binary file test-data/preprocessing_results1.pdf has changed
Binary file test-data/preprocessing_results2.ibd has changed
--- a/test-data/preprocessing_results2.imzml	Tue Oct 06 08:04:35 2020 +0000
+++ b/test-data/preprocessing_results2.imzml	Sun Nov 29 23:37:41 2020 +0000
@@ -9,8 +9,8 @@
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--- a/test-data/preprocessing_results2.imzml.txt	Tue Oct 06 08:04:35 2020 +0000
+++ b/test-data/preprocessing_results2.imzml.txt	Sun Nov 29 23:37:41 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 64
--rw-rw-r-- 1 meli meli 37404 Oct  5 19:57 ibd
--rw-rw-r-- 1 meli meli 22796 Oct  5 19:57 imzml
+-rw-rw-r-- 1 meli meli 37404 Nov 29 18:03 ibd
+-rw-rw-r-- 1 meli meli 22796 Nov 29 18:03 imzml
Binary file test-data/preprocessing_results2.pdf has changed
Binary file test-data/preprocessing_results3.ibd has changed
--- a/test-data/preprocessing_results3.imzml	Tue Oct 06 08:04:35 2020 +0000
+++ b/test-data/preprocessing_results3.imzml	Sun Nov 29 23:37:41 2020 +0000
@@ -9,9 +9,9 @@
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -143,16 +143,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="184" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="18" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="72" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="256" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="18" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="72" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="448" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -172,16 +172,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="328" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="21" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="84" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="412" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="21" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="84" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="592" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -201,16 +201,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="496" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="4" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="512" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="4" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="736" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -230,16 +230,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="528" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="18" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="72" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="600" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="18" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="72" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="880" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -259,16 +259,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="672" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="68" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="740" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="68" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1024" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -288,16 +288,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="808" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="840" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1168" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -317,16 +317,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="872" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="11" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="44" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="916" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="11" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="44" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1312" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
--- a/test-data/preprocessing_results3.imzml.txt	Tue Oct 06 08:04:35 2020 +0000
+++ b/test-data/preprocessing_results3.imzml.txt	Sun Nov 29 23:37:41 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-rw-r-- 1 meli meli   960 Oct  5 19:58 ibd
--rw-rw-r-- 1 meli meli 18112 Oct  5 19:58 imzml
+-rw-rw-r-- 1 meli meli  1456 Nov 29 18:04 ibd
+-rw-rw-r-- 1 meli meli 18133 Nov 29 18:04 imzml
Binary file test-data/preprocessing_results3.pdf has changed