Mercurial > repos > galaxyp > cardinal_spectra_plots

changeset 9:006fc980af63 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
author galaxyp
date Tue, 03 Nov 2020 22:35:49 +0000
parents 33dcc1606d53
children c56906ee67d3
files macros.xml spectra_plots.xml 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_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/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.ibd test-data/2123_auto_combined.imzml test-data/2123_auto_combined.imzml.txt test-data/2123_auto_combined_QC.pdf 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/Plot_analyze75.pdf test-data/Plot_analyze75_allpixels.pdf test-data/Plot_imzml.pdf test-data/Plot_picked.pdf test-data/Plot_processed.pdf test-data/Plot_rdata.pdf test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/analyze75_filtered2.pdf test-data/centroids_proc.pdf test-data/centroids_rdata.pdf test-data/cluster_skm.RData test-data/imzml_filtered3.pdf test-data/imzml_filtered4.pdf test-data/imzml_filtered5.pdf test-data/imzml_filtered8.pdf test-data/kmeans_analyze.pdf test-data/out3.ibd test-data/out3.imzml test-data/out3.imzml.txt test-data/out4.ibd test-data/out4.imzml test-data/out4.imzml.txt test-data/out5.ibd test-data/out5.imzml test-data/out5.imzml.txt test-data/out6.ibd test-data/out6.imzml test-data/out6.imzml.txt test-data/out7.ibd test-data/out7.imzml test-data/out7.imzml.txt test-data/out8.ibd test-data/out8.imzml test-data/out8.imzml.txt test-data/pca_imzml.pdf test-data/picked.ibd test-data/picked.imzml test-data/picked.imzml.txt test-data/picked_QC.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 test-data/preprocessing_results4.ibd test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt test-data/preprocessing_results4.pdf test-data/preprocessing_results5.ibd test-data/preprocessing_results5.imzml test-data/preprocessing_results5.imzml.txt test-data/preprocessing_results5.pdf test-data/rdata_notfiltered.pdf test-data/test1.pdf test-data/test2.pdf test-data/test2.rdata test-data/test3.pdf test-data/test4.pdf test-data/test4.rdata test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata
diffstat 101 files changed, 187 insertions(+), 182 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed May 13 17:57:37 2020 +0000
+++ b/macros.xml	Tue Nov 03 22:35:49 2020 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@VERSION@">2.4.0</token>
+    <token name="@VERSION@">2.6.0</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
-            <requirement type="package" version="3.6.1">r-base</requirement>
+            <!--requirement type="package" version="3.6.1">r-base</requirement-->
             <yield/>
         </requirements>
     </xml>
@@ -117,6 +117,13 @@
     <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ 
 ########################### QC numbers ########################
 ## including intensity calculations which need data in RAM
+
+	int_matrix = as.matrix(spectra(msidata)) ## only load once into RAM, then re-use
+	## Number of NA in spectra matrix
+        NAcount = sum(is.na(int_matrix))
+	## replace NA with zero to calculate data properties based on intensity matrix, no change in msidata
+	int_matrix[is.na(int_matrix)] <- 0
+	
         ## Number of features (mz)
         maxfeatures = length(features(msidata))
         ## Range mz
@@ -131,14 +138,12 @@
         minimumy = min(coord(msidata)[,2])
         maximumy = max(coord(msidata)[,2])
         ## Range of intensities
-        minint = round(min(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2)
-        maxint = round(max(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2)
+        minint = round(min(int_matrix), digits=2)
+        maxint = round(max(int_matrix), digits=2)
         ## Number of intensities > 0, for if conditions
-        npeaks= sum(as.matrix(spectra(msidata))>0, na.rm=TRUE)
+        npeaks= sum(int_matrix>0)
         ## Number of NA in spectra matrix
-        NAcount = sum(is.na(spectra(msidata)))
-        ## Number of NA in spectra matrix
-        infcount = sum(is.infinite(as.matrix(spectra(msidata))))
+        infcount = sum(is.infinite(int_matrix))
         ## Number of duplicated coordinates
         dupl_coord = sum(duplicated(coord(msidata)))
         properties = c("Number of m/z features",
@@ -175,7 +180,7 @@
 
             - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
             - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
-            - Cardinal "MSImageSet" data saved as .RData
+            - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData
     ]]></token>
     <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
         - Optional tabular file with m/z values: 
@@ -243,7 +248,7 @@
             </param>
             <when value="no_processed"/>
             <when value="processed">
-                <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
+                <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned"/>
                 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
                     <option value="mz" >mz</option>
                     <option value="ppm" selected="True" >ppm</option>
--- a/spectra_plots.xml	Wed May 13 17:57:37 2020 +0000
+++ b/spectra_plots.xml	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.0">
+<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.1">
     <description>
         mass spectrometry imaging mass spectra plots
     </description>
@@ -6,9 +6,9 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.2.1">r-ggplot2</requirement>
+        <requirement type="package" version="3.3.2">r-ggplot2</requirement>
         <requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="1.0.0">r-scales</requirement>
+        <requirement type="package" version="1.1.1">r-scales</requirement>
     </expand>
     <command detect_errors="exit_code">
     <![CDATA[
@@ -82,7 +82,7 @@
                 merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y"), all.x=TRUE)
                 merged_annotation[is.na(merged_annotation)] = "NA"
                 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
-                msidata\$annotation = as.factor(merged_annotation[,4])
+                msidata\$annotation = factor(merged_annotation[,4], levels = unique(as.character(merged_annotation[,4]))) ## keep the right order
 
                     ## overview plot over annotated samples
                     number_combined = length(levels(msidata\$annotation))
@@ -214,7 +214,7 @@
 
                     #if $fullmz:
                     ## plot full mz for single tabular mz
-                        print(plot(msidata, coord=list(x=x_coord, y=y_coord), key=TRUE, grid = $grid_variable))
+                        print(plot(msidata, coord=list(x=x_coord, y=y_coord), key=TRUE, grid = $grid_variable, col="black"))
                     #end if
 
                     pixelname = paste0("x = ", x_coord,", ", "y = ", y_coord)
@@ -261,7 +261,7 @@
                 }
 
                     ## print single tabular mz; manual zoom
-                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax)))
+                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black"))
 
                 #end for
 
@@ -306,7 +306,7 @@
                             }
 
                                 ## print single tabular mz; tabular zoom
-                                print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c(xlimmin,xlimmax)))
+                                print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c(xlimmin,xlimmax), col="black"))
                             }
                         }
 
@@ -329,7 +329,7 @@
 
                     #if $fullmz:
 
-                        print(plot(msidata, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", grid = $grid_variable))
+                        print(plot(msidata, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", grid = $grid_variable, col="black"))
                     #end if
 
         ##################### II) Sample: plot zoom-in mass spectrum ##########
@@ -366,7 +366,7 @@
                         }
                 }
 
-                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, main="Average spectrum", run = "infile", strip=FALSE, key=TRUE, xlim= c($token.xlimmin,$token.xlimmax)))
+                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, main="Average spectrum", run = "infile", strip=FALSE, key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black"))
 
             #end for
 
@@ -401,7 +401,7 @@
                                     }
                                 )   
 
-                        print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", xlim= c(xlimmin,xlimmax)))
+                        print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", xlim= c(xlimmin,xlimmax), col="black"))
                 }
             }
 
@@ -456,7 +456,7 @@
         <expand macro="reading_msidata"/>
         <expand macro="pdf_filename"/>
         <conditional name="pixel_conditional">
-            <param name="pixel_type" type="select" label="Choose spectra (pixel)">
+            <param name="pixel_type" type="select" label="Choose spectra (pixel) and/or add spectra annotations">
                 <option value="all_pixel" selected="True" >All spectra</option>
                 <option value="tabular_pixel">Single spectra</option>
             </param>
@@ -588,7 +588,7 @@
             <expand macro="processed_infile_imzml"/>
             <conditional name="processed_cond">
                 <param name="processed_file" value="processed"/>
-                <param name="accuracy" value="50"/>
+                <param name="accuracy" value="100"/>
                 <param name="units" value="ppm"/>
             </conditional>
             <conditional name="pixel_conditional">
Binary file test-data/112_auto_combined.ibd has changed
--- a/test-data/112_auto_combined.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/112_auto_combined.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -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="de720b1f-c3fa-4596-b054-284efaff29fc" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="040b9782d76e25ebe9a6b7c27fdda7e27e711674" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="23f1e1c8-aaa5-4d04-ab81-da14f7d24507" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="b2e009b6e72791420e704b751b4fc1a0f36bf420" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/112_auto_combined.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/112_auto_combined.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 556
--rw-r--r-- 1 meli meli 537552 Apr 21 12:46 ibd
--rw-r--r-- 1 meli meli  27497 Apr 21 12:46 imzml
+-rw-rw-r-- 1 meli meli 537552 Aug 30 13:50 ibd
+-rw-rw-r-- 1 meli meli  27497 Aug 30 13:50 imzml
Binary file test-data/112_auto_combined_QC.pdf has changed
Binary file test-data/123_combined.ibd has changed
--- a/test-data/123_combined.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/123_combined.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -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="c9f19079-a92c-4995-b4ee-48d2766994a8" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="889b1020d3d844330f13a360be4b2bd0b65d11a1" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="383dcc6e-fa4e-4ffe-8523-9cd0c3bd2571" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2cd98028c7ab9bd53b698168b508a0ac74f256c9" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/123_combined.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/123_combined.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 452
--rw-r--r-- 1 meli meli 436764 Apr 21 12:41 ibd
--rw-r--r-- 1 meli meli  22855 Apr 21 12:41 imzml
+-rw-rw-r-- 1 meli meli 436764 Aug 30 13:46 ibd
+-rw-rw-r-- 1 meli meli  22855 Aug 30 13:46 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	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/123_combined_auto.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -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="386d1a7c-e065-4bf1-96a6-019586133b29" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9bdafd878211e7d0c8fd0ef11bd534cbacfe7d40" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="ae23e625-6ac2-4a33-be4a-b73af67bc0dd" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1b81e4b14567ea9da1177c0490f636d0823b2aac" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/123_combined_auto.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/123_combined_auto.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 452
--rw-r--r-- 1 meli meli 436764 Apr 21 12:43 ibd
--rw-r--r-- 1 meli meli  22860 Apr 21 12:43 imzml
+-rw-rw-r-- 1 meli meli 436764 Aug 30 13:48 ibd
+-rw-rw-r-- 1 meli meli  22860 Aug 30 13:48 imzml
Binary file test-data/123_combined_auto.pdf has changed
Binary file test-data/12_combined.ibd has changed
--- a/test-data/12_combined.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/12_combined.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -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="57f26041-833d-4843-ba25-0037f2c35f51" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c271b37214900da9960cd3bcb748cc5bc377cfec" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="85ec7820-8e87-4fb2-b74a-5b9cd8cf24d6" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d8a4e14091441873e8969f3b6b249f55b4d95146" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/12_combined.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/12_combined.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 352
--rw-r--r-- 1 meli meli 335976 Apr 21 12:45 ibd
--rw-r--r-- 1 meli meli  18225 Apr 21 12:45 imzml
+-rw-rw-r-- 1 meli meli 335976 Aug 30 13:49 ibd
+-rw-rw-r-- 1 meli meli  18225 Aug 30 13:49 imzml
Binary file test-data/12_combined_QC.pdf has changed
Binary file test-data/2123_auto_combined.ibd has changed
--- a/test-data/2123_auto_combined.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/2123_auto_combined.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -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="1c0a127a-8417-47ef-a049-553b9d56de81" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5113bf7d09e0b1a584238aa6c5242f50eeef839b" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="d5abe155-9afd-4249-aaf3-8fc631c1fd10" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="3c93096f299dc50ca088d712feca19f8bf2d5152" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/2123_auto_combined.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/2123_auto_combined.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 656
--rw-r--r-- 1 meli meli 638340 Apr 21 12:46 ibd
--rw-r--r-- 1 meli meli  32132 Apr 21 12:46 imzml
+-rw-rw-r-- 1 meli meli 638340 Aug 30 13:50 ibd
+-rw-rw-r-- 1 meli meli  32132 Aug 30 13:50 imzml
Binary file test-data/2123_auto_combined_QC.pdf has changed
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/Plot_analyze75.pdf has changed
Binary file test-data/Plot_analyze75_allpixels.pdf has changed
Binary file test-data/Plot_imzml.pdf has changed
Binary file test-data/Plot_picked.pdf has changed
Binary file test-data/Plot_processed.pdf has changed
Binary file test-data/Plot_rdata.pdf has changed
Binary file test-data/QC_analyze75.pdf has changed
Binary file test-data/QC_empty_spectra.pdf has changed
Binary file test-data/QC_imzml.pdf has changed
Binary file test-data/QC_rdata.pdf has changed
Binary file test-data/analyze75_filtered2.pdf has changed
Binary file test-data/centroids_proc.pdf has changed
Binary file test-data/centroids_rdata.pdf has changed
Binary file test-data/cluster_skm.RData has changed
Binary file test-data/imzml_filtered3.pdf has changed
Binary file test-data/imzml_filtered4.pdf has changed
Binary file test-data/imzml_filtered5.pdf has changed
Binary file test-data/imzml_filtered8.pdf has changed
Binary file test-data/kmeans_analyze.pdf has changed
Binary file test-data/out3.ibd has changed
--- a/test-data/out3.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out3.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -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="7cde7a72-9a6b-4ed9-a809-79ca20bf45b4" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4a26497a6ddfc9a61e9c0e463e4c246c5d734f80" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="97f42eea-750c-49e4-b46d-08c548dc3b9d" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4e046226f81e9c78255df625ca3546ef26dd0693" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/out3.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out3.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-r--r-- 1 meli meli 9616 Mär 24 20:25 ibd
--rw-r--r-- 1 meli meli 8958 Mär 24 20:25 imzml
+-rw-rw-r-- 1 meli meli 9616 Sep 27 10:51 ibd
+-rw-rw-r-- 1 meli meli 8958 Sep 27 10:51 imzml
Binary file test-data/out4.ibd has changed
--- a/test-data/out4.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out4.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -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="b0dec95e-b66f-4c3f-86df-166d942f42c3" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d9b557cf2c0e15a0cdd863e50897b07a55a26f31" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="37f3f75a-82c4-47c5-b78e-28fb8697e59b" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1746fd2ec8a12707330a78ff5a0ff98cb53dca42" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/out4.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out4.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 44
--rw-r--r-- 1 meli meli 28792 Mär 24 19:23 ibd
--rw-r--r-- 1 meli meli 12046 Mär 24 19:23 imzml
+-rw-rw-r-- 1 meli meli 28792 Sep 27 10:52 ibd
+-rw-rw-r-- 1 meli meli 12046 Sep 27 10:52 imzml
Binary file test-data/out5.ibd has changed
--- a/test-data/out5.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out5.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -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="87b0ab73-abe6-4eb6-91ba-b6d493a343bc" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9de3a02d0943ecda0717845511a8f7b8f58d1db7" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="37236c7e-6e93-4ccc-9111-1b1153aac713" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ccb886aaf3cb7564f518884413ea988c59a1de57" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/out5.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out5.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 20
--rw-r--r-- 1 meli meli   380 Mär 24 19:24 ibd
--rw-r--r-- 1 meli meli 13525 Mär 24 19:24 imzml
+-rw-rw-r-- 1 meli meli   380 Sep 27 10:53 ibd
+-rw-rw-r-- 1 meli meli 13525 Sep 27 10:53 imzml
Binary file test-data/out6.ibd has changed
--- a/test-data/out6.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out6.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -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="8b625a26-987e-4e32-b7d4-729efe840814" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="78e6eb56507d789575ee0495e60f9d44a192c0dd" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="734d4b50-4440-4747-a0e9-de78974d1487" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="b1636b28fd4e0ab9caf5aaa4c1a40760030a4e73" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/out6.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out6.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 164
--rw-r--r-- 1 meli meli 146896 Mär 24 19:25 ibd
--rw-r--r-- 1 meli meli  18221 Mär 24 19:25 imzml
+-rw-rw-r-- 1 meli meli 146896 Sep 27 10:53 ibd
+-rw-rw-r-- 1 meli meli  18221 Sep 27 10:53 imzml
Binary file test-data/out7.ibd has changed
--- a/test-data/out7.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out7.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -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="bf61653e-aa1a-4f9a-a84d-3ff3435ee7fe" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="352c33defde6728b7dfb83e18ed1c433fa4b8697" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="f81632b3-50b0-4a57-88a2-5f7cf97f9bae" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9f88294c3cff3e8c30e80632d6ad616b7db18089" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/out7.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out7.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 116
--rw-r--r-- 1 meli meli 95976 Mär 24 19:26 ibd
--rw-r--r-- 1 meli meli 18199 Mär 24 19:26 imzml
+-rw-rw-r-- 1 meli meli 95976 Sep 27 10:54 ibd
+-rw-rw-r-- 1 meli meli 18199 Sep 27 10:54 imzml
Binary file test-data/out8.ibd has changed
--- a/test-data/out8.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out8.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -9,9 +9,9 @@
 		<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="ace74b18-25e2-4722-89f4-6eedc2b62ed8" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="41d580d8acf3e67df8b63f001fe941da7334861b" />
-			<cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="02059ae7-7beb-4ecf-92ae-7a767e04bf43" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="dc3960918fa3008824889b4ac142be1d0534ded8" />
+			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
 	<referenceableParamGroupList count="4">
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
@@ -90,15 +90,15 @@
 					<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" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33612" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="41484" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -118,16 +118,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100804" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="82952" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -147,16 +147,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="124420" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -176,16 +176,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="165888" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -205,16 +205,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="268784" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="207356" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
--- a/test-data/out8.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/out8.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
-total 348
--rw-r--r-- 1 meli meli 335976 Mär 24 19:27 ibd
--rw-r--r-- 1 meli meli  12402 Mär 24 19:27 imzml
+total 260
+-rw-rw-r-- 1 meli meli 248824 Sep 27 11:44 ibd
+-rw-rw-r-- 1 meli meli  12397 Sep 27 11:44 imzml
Binary file test-data/pca_imzml.pdf has changed
Binary file test-data/picked.ibd has changed
--- a/test-data/picked.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/picked.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -8,8 +8,8 @@
  <fileDescription>
   <fileContent>
    <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
-   <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{cb7c9edc-eee3-4159-a8a1-efdf5fc56a13}"/>
-   <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="f3e61f4699108e65bb678cfbbd6208be562f11c9"/>
+   <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{19bd2a62-4cc1-4316-b173-25f1de3871f6}"/>
+   <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ca84032e28aa3c04e4f41b74b85ccd1bd6e44107"/>
    <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
    <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/>
   </fileContent>
--- a/test-data/picked.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/picked.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 192
--rw-r--r-- 1 meli meli 157984 Apr 21 12:42 ibd
--rw-r--r-- 1 meli meli  35012 Apr 21 12:42 imzml
+-rw-rw-r-- 1 meli meli 157984 Aug 30 13:47 ibd
+-rw-rw-r-- 1 meli meli  35012 Aug 30 13:47 imzml
Binary file test-data/picked_QC.pdf has changed
Binary file test-data/preprocessing_results1.ibd has changed
--- a/test-data/preprocessing_results1.imzml	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/preprocessing_results1.imzml	Tue Nov 03 22:35:49 2020 +0000
@@ -9,8 +9,8 @@
 		<fileContent>
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+++ b/test-data/preprocessing_results1.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
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 total 24
--rw-r--r-- 1 meli meli   216 Mai 10 17:37 ibd
--rw-r--r-- 1 meli meli 18090 Mai 10 17:37 imzml
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--- a/test-data/preprocessing_results2.imzml	Wed May 13 17:57:37 2020 +0000
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@@ -1,4 +1,4 @@
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Binary file test-data/preprocessing_results3.ibd has changed
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@@ -1,4 +1,4 @@
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--- a/test-data/preprocessing_results4.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/preprocessing_results4.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
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--- a/test-data/preprocessing_results5.imzml	Wed May 13 17:57:37 2020 +0000
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--- a/test-data/preprocessing_results5.imzml.txt	Wed May 13 17:57:37 2020 +0000
+++ b/test-data/preprocessing_results5.imzml.txt	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
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--rw-r--r-- 1 meli meli 415936 Mai 10 17:40 ibd
--rw-r--r-- 1 meli meli  18569 Mai 10 17:40 imzml
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