Mercurial > repos > galaxyp > cardinal_preprocessing

changeset 9:ca727a6dede6 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 11:43:31 +0000
parents 87bb011a4ee8
children 5abc3ab4792c
files macros.xml preprocessing.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_results4.imzml test-data/preprocessing_results4.imzml.txt test-data/preprocessing_results4.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 84 files changed, 163 insertions(+), 165 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed May 13 14:21:48 2020 -0400
+++ b/macros.xml	Thu Sep 24 11:43:31 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>
@@ -175,7 +175,7 @@
 
             - 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 +243,7 @@
             </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/preprocessing.xml	Wed May 13 14:21:48 2020 -0400
+++ b/preprocessing.xml	Thu Sep 24 11:43:31 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.2">
+<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.0">
     <description>
         mass spectrometry imaging preprocessing
     </description>
@@ -7,7 +7,7 @@
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.2.1">r-ggplot2</requirement>
+        <requirement type="package" version="3.3.2">r-ggplot2</requirement>
     </expand>
     <command detect_errors="exit_code">
     <![CDATA[
@@ -347,35 +347,37 @@
             title("Spectra after peak binning", outer=TRUE, line=0)
 
 
-    ############################### Data reduction ###########################
+    ############################### Mass binning ###########################
 
-        #elif str( $method.methods_conditional.preprocessing_method) == 'Data_reduction':
-            print('Data_reduction')
+        #elif str( $method.methods_conditional.preprocessing_method) == 'Mass_binning':
+            print('mass binning')
 
-            ## these functions only work on MSImageSet
-            msidata = as(msidata, "MSImageSet")
+            #if str( $method.methods_conditional.mz_range.features_filtering) == 'change_mz_range':
+
+                #if str($processed_cond.processed_file) == "processed":
 
-            #if str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'bin':
-                print('bin reduction')
+                msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)
+                
+                #else 
+                    msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)
+                #end if
+
+		   
+	    #elif str( $method.methods_conditional.mz_range.features_filtering) == 'none':	    
 
-                msidata = reduceDimension(msidata, method="bin", width=$method.methods_conditional.methods_for_reduction.bin_width, units="$method.methods_conditional.methods_for_reduction.bin_units", fun=$method.methods_conditional.methods_for_reduction.bin_fun)
+                msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)
 
+            #end if
+             
+            msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
+                
                 ## optional: replace NA with 0
-                #if $method.methods_conditional.methods_for_reduction.replace_NA_bin:
+                #if $method.methods_conditional.replace_NA_bin:
                     ## count and replace NAs
                     print(paste0("Number of NA that were set to zero after binning:",sum(is.na(spectra(msidata)))))
                     spectra(msidata)[is.na(spectra(msidata))] = 0 
                 #end if
-
-            #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'resample':
-                print('resample reduction')
-
-                msidata = reduceDimension(msidata, method="resample", step=$method.methods_conditional.methods_for_reduction.resample_step)
-            #end if
-
-            ## coercition into new format
-            msidata = as(msidata, "MSImagingExperiment")
-
+                
             ############################### QC ###########################
 
             maxfeatures =nrow(msidata)
@@ -386,7 +388,7 @@
             QC_numbers= cbind(QC_numbers, reduced)
             vectorofactions = append(vectorofactions, "reduced")
             print(plot(msidata, pixel=random_spectra))
-            title("Spectra after data reduction", outer=TRUE, line=0)
+            title("Spectra after m/z binning", outer=TRUE, line=0)
 
         ############################### Transformation ###########################
 
@@ -479,7 +481,7 @@
                     <option value="Peak_alignment">Peak alignment</option>
                     <option value="Peak_filtering">Peak filtering</option>
                     <option value="Peak_binning">Peak binning to reference peaks</option>
-                    <option value="Data_reduction">Data reduction</option>
+                    <option value="Mass_binning">m/z binning</option>
                     <option value="Transformation">Transformation</option>
                 </param>
                 <when value="Normalization">
@@ -620,31 +622,29 @@
                             <option value="area">area</option>
                     </param>
                 </when>
-                <when value="Data_reduction">
-                    <conditional name="methods_for_reduction">
-                        <param name="reduction_method" type="select" label="Reduction method">
-                            <option value="bin" selected="True">bin</option>
-                            <option value="resample">resample</option>
+                <when value="Mass_binning">
+                    <param name="bin_width" type="float" value="1" label="The width of a bin in m/z or ppm" help="Width must be greater than range of m/z values divided by number of m/z features"/>
+		    <param name="bin_units" type="select" display="radio"
+		           label="Unit for bin">
+		            <option value="mz" selected="True">mz</option>
+		            <option value="ppm">ppm</option>
+		    </param>
+                    <param name="bin_fun" type="select" display="radio"
+                           label="Calculate sum or mean intensity for ions of the same bin">
+                            <option value="mean" selected="True">mean</option>
+                            <option value="sum">sum</option>
+                    </param>
+                    <param name="replace_NA_bin" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Binning can introduce NAs, should they be replaced with 0"/>
+                    <conditional name="mz_range">
+            		 <param name="features_filtering" type="select" label="Select m/z feature filtering option">
+                            <option value="none" selected="True">none</option>
+                            <option value="change_mz_range">change m/z range</option>
                         </param>
-                        <when value="bin">
-                            <param name="bin_width" type="float" value="1"
-                                   label="The width of a bin in m/z or ppm" help="Width must be greater than range of m/z values divided by number of m/z features"/>
-                            <param name="bin_units" type="select" display="radio"
-                                   label="Unit for bin">
-                                    <option value="mz" selected="True">mz</option>
-                                    <option value="ppm">ppm</option>
-                            </param>
-                            <param name="bin_fun" type="select" display="radio"
-                                   label="Calculate sum or mean intensity for ions of the same bin">
-                                    <option value="mean" selected="True">mean</option>
-                                    <option value="sum">sum</option>
-                            </param>
-                            <param name="replace_NA_bin" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Binning can introduce NAs, should they be replaced with 0"/>
-                        </when>
-                        <when value="resample">
-                            <param name="resample_step" type="float" value="1"
-                                   label="The step size in m/z" help="Step size must be greater than range of m/z values divided by number of m/z features"/>
-                        </when>
+			    <when value="none"/>
+			    <when value="change_mz_range">
+				<param name="min_mz" type="float" value="1" label="Minimum value for m/z"/>
+				<param name="max_mz" type="float" value="10000" label="Maximum value for m/z"/>
+			    </when>
                     </conditional>
                 </when>
                 <when value="Transformation">
@@ -800,11 +800,9 @@
             </repeat>
             <repeat name="methods">
                 <conditional name="methods_conditional">
-                    <param name="preprocessing_method" value="Data_reduction"/>
-                    <conditional name="methods_for_reduction">
-                        <param name="reduction_method" value="bin"/>
+                    <param name="preprocessing_method" value="Mass_binning"/>
                         <param name="bin_width" value="0.1"/>
-                    </conditional>
+                        <param name="bin_units" value="mz"/>
                 </conditional>
             </repeat>
             <output name="QC_overview" file="preprocessing_results4.pdf" compare="sim_size"/>
@@ -817,7 +815,7 @@
             <expand macro="processed_infile_imzml"/>
             <conditional name="processed_cond">
                 <param name="processed_file" value="processed"/>
-                <param name="accuracy" value="100"/>
+                <param name="accuracy" value="200"/>
                 <param name="units" value="ppm"/>
             </conditional>
             <repeat name="methods">
Binary file test-data/112_auto_combined.ibd has changed
--- a/test-data/112_auto_combined.imzml	Wed May 13 14:21:48 2020 -0400
+++ b/test-data/112_auto_combined.imzml	Thu Sep 24 11:43:31 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 14:21:48 2020 -0400
+++ b/test-data/112_auto_combined.imzml.txt	Thu Sep 24 11:43:31 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 14:21:48 2020 -0400
+++ b/test-data/123_combined.imzml	Thu Sep 24 11:43:31 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 14:21:48 2020 -0400
+++ b/test-data/123_combined.imzml.txt	Thu Sep 24 11:43:31 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 14:21:48 2020 -0400
+++ b/test-data/123_combined_auto.imzml	Thu Sep 24 11:43:31 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 14:21:48 2020 -0400
+++ b/test-data/123_combined_auto.imzml.txt	Thu Sep 24 11:43:31 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 14:21:48 2020 -0400
+++ b/test-data/12_combined.imzml	Thu Sep 24 11:43:31 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 14:21:48 2020 -0400
+++ b/test-data/12_combined.imzml.txt	Thu Sep 24 11:43:31 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 14:21:48 2020 -0400
+++ b/test-data/2123_auto_combined.imzml	Thu Sep 24 11:43:31 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 14:21:48 2020 -0400
+++ b/test-data/2123_auto_combined.imzml.txt	Thu Sep 24 11:43:31 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 14:21:48 2020 -0400
+++ b/test-data/out3.imzml	Thu Sep 24 11:43:31 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="c6cc990a-d910-4c17-aedd-ceb204b4d105" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ef8c4f864d0386736c986ebb4d4eb29a726e42d4" />
 			<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 14:21:48 2020 -0400
+++ b/test-data/out3.imzml.txt	Thu Sep 24 11:43:31 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 Aug 23 17:39 ibd
+-rw-rw-r-- 1 meli meli 8958 Aug 23 17:39 imzml
Binary file test-data/out4.ibd has changed
--- a/test-data/out4.imzml	Wed May 13 14:21:48 2020 -0400
+++ b/test-data/out4.imzml	Thu Sep 24 11:43:31 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="78fa5a7c-8dc8-4ff1-ad77-b19714f285cb" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="64d40f8c65af1399e24d94569f4dd3fdbf43a901" />
 			<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 14:21:48 2020 -0400
+++ b/test-data/out4.imzml.txt	Thu Sep 24 11:43:31 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 Aug 23 17:39 ibd
+-rw-rw-r-- 1 meli meli 12046 Aug 23 17:39 imzml
Binary file test-data/out5.ibd has changed
--- a/test-data/out5.imzml	Wed May 13 14:21:48 2020 -0400
+++ b/test-data/out5.imzml	Thu Sep 24 11:43:31 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="30751422-deca-429e-9f8e-24639c108d6d" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2c7f19c6447844039a112152c19f7cfd50dbf12e" />
 			<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 14:21:48 2020 -0400
+++ b/test-data/out5.imzml.txt	Thu Sep 24 11:43:31 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 Aug 23 17:40 ibd
+-rw-rw-r-- 1 meli meli 13525 Aug 23 17:40 imzml
Binary file test-data/out6.ibd has changed
--- a/test-data/out6.imzml	Wed May 13 14:21:48 2020 -0400
+++ b/test-data/out6.imzml	Thu Sep 24 11:43:31 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="254b991f-92f5-46d5-8069-6f9ecd53b05a" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0aaa784dc2a335da176a4bc2d12a43f2d18bdbf1" />
 			<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 14:21:48 2020 -0400
+++ b/test-data/out6.imzml.txt	Thu Sep 24 11:43:31 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 Aug 23 17:41 ibd
+-rw-rw-r-- 1 meli meli  18221 Aug 23 17:41 imzml
Binary file test-data/out7.ibd has changed
--- a/test-data/out7.imzml	Wed May 13 14:21:48 2020 -0400
+++ b/test-data/out7.imzml	Thu Sep 24 11:43:31 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="227ecc2e-a494-4018-afc5-45eaa790e812" />
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 			<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 14:21:48 2020 -0400
+++ b/test-data/out7.imzml.txt	Thu Sep 24 11:43:31 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 Aug 23 17:41 ibd
+-rw-rw-r-- 1 meli meli 18199 Aug 23 17:41 imzml
Binary file test-data/out8.ibd has changed
--- a/test-data/out8.imzml	Wed May 13 14:21:48 2020 -0400
+++ b/test-data/out8.imzml	Thu Sep 24 11:43:31 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="ace74b18-25e2-4722-89f4-6eedc2b62ed8" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="41d580d8acf3e67df8b63f001fe941da7334861b" />
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 			<cvParam cvRef="IMS" accession="IMS:1000031" name="processed" 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/out8.imzml.txt	Wed May 13 14:21:48 2020 -0400
+++ b/test-data/out8.imzml.txt	Thu Sep 24 11:43:31 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
+-rw-rw-r-- 1 meli meli 335976 Aug 23 17:42 ibd
+-rw-rw-r-- 1 meli meli  12402 Aug 23 17:42 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 14:21:48 2020 -0400
+++ b/test-data/picked.imzml	Thu Sep 24 11:43:31 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}"/>
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    <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 14:21:48 2020 -0400
+++ b/test-data/picked.imzml.txt	Thu Sep 24 11:43:31 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
--- a/test-data/preprocessing_results4.imzml	Wed May 13 14:21:48 2020 -0400
+++ b/test-data/preprocessing_results4.imzml	Thu Sep 24 11:43:31 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="c6122884-ceb5-46b6-9160-5d28e8862946" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="03e4b58b8e63517605164e90b85fe93a851a9c5b" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9a685278-3bf0-48b5-b7c7-73a7a92625b2" />
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 			<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>
@@ -86,15 +86,15 @@
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
 						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1567" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6268" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />
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+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1567" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6268" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -115,15 +115,15 @@
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
 						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1567" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6268" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
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-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="12552" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1567" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6268" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -144,15 +144,15 @@
 					<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="1581" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1567" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6268" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="18988" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="18820" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1567" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6268" />
 						<binary />
 					</binaryDataArray>
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@@ -173,15 +173,15 @@
 					<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="1581" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1567" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6268" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="25088" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1567" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6268" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -202,15 +202,15 @@
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@@ -289,15 +289,15 @@
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+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1567" />
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--- a/test-data/preprocessing_results4.imzml.txt	Wed May 13 14:21:48 2020 -0400
+++ b/test-data/preprocessing_results4.imzml.txt	Thu Sep 24 11:43:31 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 84
--rw-r--r-- 1 meli meli 63256 Mai 10 17:40 ibd
--rw-r--r-- 1 meli meli 18199 Mai 10 17:40 imzml
+-rw-rw-r-- 1 meli meli 62696 Sep 20 11:48 ibd
+-rw-rw-r-- 1 meli meli 18199 Sep 20 11:48 imzml
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