Mercurial > repos > galaxyp > cardinal_combine

changeset 2:7b07fee610fc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
author galaxyp
date Fri, 15 Feb 2019 10:12:32 -0500
parents ac474da43605
children 1ba687b2b748
files combine.xml macros.xml test-data/112_auto_combined.RData test-data/112_auto_combined.ibd test-data/112_auto_combined.imzml test-data/112_auto_combined.imzml.txt test-data/112_auto_combined_QC.pdf test-data/123_annotation.ibd test-data/123_annotation.imzml test-data/123_auto_combined.imzml.txt test-data/123_combined.RData test-data/123_combined_QC.pdf test-data/123_combined_auto.ibd test-data/123_combined_auto.imzml test-data/123_combined_auto.imzml.txt test-data/123_combined_auto.pdf test-data/123_combined_auto.tabular test-data/12_combined.RData test-data/12_combined_QC.pdf test-data/2123_auto_combined.RData test-data/2123_auto_combined_QC.pdf test-data/Plot_empty_spectra.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/analyze_filtered.RData test-data/analyze_filtered.pdf test-data/analyze_filteredoutside.RData test-data/analyze_originaloutput.RData test-data/analyze_originaloutput2.RData test-data/centroids_rdata.pdf test-data/cluster_skm.RData test-data/features_test2.tabular test-data/features_test4.tabular test-data/features_test6.tabular test-data/features_test7.tabular test-data/imzml_filtered.RData test-data/imzml_filtered.pdf test-data/imzml_filtered3.RData test-data/imzml_filtered3.pdf test-data/imzml_filtered4.RData test-data/imzml_filtered4.pdf test-data/imzml_filtered5.RData test-data/imzml_filtered5.pdf test-data/kmeans_analyze.pdf test-data/loadings_pca.tabular 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/pca_imzml.pdf test-data/pixel_out2.tabular test-data/pixel_out3.tabular test-data/preprocessed.rdata test-data/preprocessing_results1.RData test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results1.pdf test-data/preprocessing_results1.txt test-data/preprocessing_results2.RData test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results2.pdf test-data/preprocessing_results2.txt test-data/preprocessing_results3.RData 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.RData test-data/preprocessing_results4.ibd test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt test-data/preprocessing_results4.pdf test-data/preprocessing_results4.txt test-data/preprocessing_results5.RData test-data/preprocessing_results5.pdf test-data/preprocessing_results5.txt test-data/rdata_notfiltered.RData test-data/rdata_notfiltered.pdf test-data/scores_pca.tabular 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 107 files changed, 4360 insertions(+), 2160 deletions(-) [+]
line wrap: on
line diff
--- a/combine.xml	Thu Oct 25 07:22:08 2018 -0400
+++ b/combine.xml	Fri Feb 15 10:12:32 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.1">
+<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.2">
     <description>
         combine several mass spectrometry imaging datasets into one
     </description>
@@ -30,9 +30,8 @@
 
         cat '${msi_combine}' &&
         Rscript '${msi_combine}' &&
-        #if $imzml_output:
+        #if str($imzml_output) == "imzml_format":
             mkdir $outfile_imzml.files_path &&
-            ls -l &&
             mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
             mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
         #end if
@@ -167,7 +166,8 @@
         ## use name of Galaxy inputfile as combined sample annotation
         names_vector = character()
         #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier))
-        if (sum(spectra(msidata_$i)[],na.rm=TRUE)>0) ## use only valid files
+
+        if (ncol(msidata_$i)>0 & nrow(msidata_$i) >0)
         {
             if (is.null(levels(msidata_$i\$combined_sample)))
             {
@@ -194,8 +194,7 @@
     ## store files to combine them later and for each file check if it is valid
 
     #silent $msidata.append('msidata_'+str($i))
-    valid_dataset = append(valid_dataset, 
-         (ncol(msidata_$i)>0 & nrow(msidata_$i)>0 & sum(spectra(msidata_$i)[], na.rm=TRUE)>0))
+    valid_dataset = append(valid_dataset, ncol(msidata_$i)>0 & nrow(msidata_$i)>0) ## file with no intensities is considered valid
 
 #end for
 
@@ -217,13 +216,15 @@
     position_df = cbind(coord(msidata_combined)[,1:2], msidata_combined\$combined_sample)
     colnames(position_df)[3] = "sample_name"
 
-     ## save as (.RData)
     msidata = msidata_combined
-    save(msidata, file="$msidata_combined")
 
     ## save msidata as imzML file
-    #if $imzml_output:
+    #if str($imzml_output) == "imzml_format":
         writeImzML(msidata, "out")
+    #elif str($imzml_output) == "rdata_format":
+        ## save as (.RData)
+        iData(msidata) = iData(msidata)[]
+        save(msidata, file="$outfile_rdata")
     #end if
 
 
@@ -251,17 +252,19 @@
 
     msidata_combined = do.call(combine, datasetlist)
 
-    ## save as (.RData)
-
     msidata = msidata_combined
-    save(msidata, file="$msidata_combined")
-
     ## save msidata as imzML file
-    writeImzML(msidata, "out")
+    #if str($imzml_output) == "imzml_format":
+        writeImzML(msidata, "out")
+    #elif str($imzml_output) == "rdata_format":
+        ## save as (.RData)
+        iData(msidata) = iData(msidata)[]
+        save(msidata, file="$outfile_rdata")
+    #end if
 
     ## create x,y,sample_name dataframe for QC pdf
 
-    position_df = cbind(coord(msidata), msidata\$combined_sample)
+    position_df = cbind(coord(msidata)[,1:2], msidata\$combined_sample)
     colnames(position_df)[3] = "sample_name"
 
 #end if
@@ -272,8 +275,6 @@
 
 ########### QC with pixels and their annotations ################################
 
-print(paste0("Number of NA in input file: ",sum(is.na(spectra(msidata)[]))))
-
 pdf("Combined_qc.pdf", width=15, height=15)
 
 ## combined plot
@@ -284,7 +285,7 @@
        theme_bw()+
        theme(text=element_text(family="ArialMT", face="bold", size=15))+
        theme(legend.position="bottom",legend.direction="vertical")+
-       guides(fill=guide_legend(ncol=5,byrow=TRUE))
+       guides(fill=guide_legend(ncol=4,byrow=TRUE))
 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
 for(file_count in 1:nrow(coord_labels))
@@ -293,12 +294,10 @@
 print(combine_plot)
 
     #if str($annotation_cond.annotation_tabular) == 'annotation'
-
         ## annotation plots
 
         ## plot 1
-
-        column1_df = cbind(coord(msidata), msidata\$column1)
+        column1_df = cbind(coord(msidata)[,1:2], msidata\$column1)
         colnames(column1_df)[3] = "column1"
 
         if (sum(is.na(column1_df[3])) < nrow(column1_df)){
@@ -309,13 +308,13 @@
                theme_bw()+
                theme(text=element_text(family="ArialMT", face="bold", size=15))+
                theme(legend.position="bottom",legend.direction="vertical")+
-               guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[1]))
+               guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[1]))
         print(column1_plot)}
         ##rename columnname for output tabular file
         colnames(column1_df)[3] = annotation_colnames[1]
 
         ## plot 2
-        column2_df = cbind(coord(msidata), msidata\$column2)
+        column2_df = cbind(coord(msidata)[,1:2], msidata\$column2)
         colnames(column2_df)[3] = "column2"
 
         if (sum(is.na(column2_df[3])) < nrow(column2_df)){
@@ -326,13 +325,14 @@
                theme_bw()+
                theme(text=element_text(family="ArialMT", face="bold", size=15))+
                theme(legend.position="bottom",legend.direction="vertical")+
-               guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[2]))
+               guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[2]))
         print(column2_plot)}
+
         ##rename columnname for output tabular file
         colnames(column2_df)[3] = annotation_colnames[2]
 
         ## plot 3
-        column3_df = cbind(coord(msidata), msidata\$column3)
+        column3_df = cbind(coord(msidata)[,1:2], msidata\$column3)
         colnames(column3_df)[3] = "column3"
         if (sum(is.na(column3_df[3])) < nrow(column3_df)){
         column3_plot = ggplot(column3_df, aes(x=x, y=y, fill=column3))+
@@ -342,13 +342,13 @@
                theme_bw()+
                theme(text=element_text(family="ArialMT", face="bold", size=15))+
                theme(legend.position="bottom",legend.direction="vertical")+
-               guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[3]))
+               guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[3]))
         print(column3_plot)}
         ##rename columnname for output tabular file
         colnames(column3_df)[3] = annotation_colnames[3]
 
         ## plot 4
-        column4_df = cbind(coord(msidata), msidata\$column4)
+        column4_df = cbind(coord(msidata)[,1:2], msidata\$column4)
         colnames(column4_df)[3] = "column4"
 
         if (sum(is.na(column4_df[3])) < nrow(column4_df)){
@@ -359,14 +359,14 @@
                theme_bw()+
                theme(text=element_text(family="ArialMT", face="bold", size=15))+
                theme(legend.position="bottom",legend.direction="vertical")+
-               guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[4]))
+               guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[4]))
         print(column4_plot)}
         ##rename columnname for output tabular file
         colnames(column4_df)[3] = annotation_colnames[4]
 
         ## plot5
 
-        column5_df = cbind(coord(msidata), msidata\$column5)
+        column5_df = cbind(coord(msidata)[,1:2], msidata\$column5)
         colnames(column5_df)[3] = "column5"
         if (sum(is.na(column5_df[3])) < nrow(column5_df)){
         column5_plot = ggplot(column5_df, aes(x=x, y=y, fill=column5))+
@@ -376,20 +376,18 @@
                theme_bw()+
                theme(text=element_text(family="ArialMT", face="bold", size=15))+
                theme(legend.position="bottom",legend.direction="vertical")+
-               guides(fill=guide_legend(ncol=5,byrow=TRUE, title=annotation_colnames[5]))
+               guides(fill=guide_legend(ncol=4,byrow=TRUE, title=annotation_colnames[5]))
         print(column5_plot)}
         ##rename columnname for output tabular file
         colnames(column5_df)[3] = annotation_colnames[5]
 
     #end if
-
     dev.off()
 
 ##################### annotation tabular output ################################
 
     if (length(features(msidata))> 0 & length(pixels(msidata)) > 0){
-
-position_df\$sample_name = gsub("^[^_]*_","",position_df\$sample_name)
+        position_df\$sample_name = gsub("^[^_]*_","",position_df\$sample_name)
 
         #if str($annotation_cond.annotation_tabular) == 'no_annotation':
 
@@ -399,7 +397,6 @@
             annotation_df_list = list(position_df, column1_df, column2_df, column3_df, column4_df, column5_df)
             combined_annotations = Reduce(function(...) merge(..., by=c("x", "y"), all=TRUE), annotation_df_list)
             write.table(combined_annotations, file="$pixel_annotations", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
-
         #end if 
 
     }else{
@@ -450,7 +447,7 @@
             </param>
             <when value="automatic_combine"/>
             <when value="xy_shifts">
-                <param name="coordinates_file" type="data" format="tabular" label="datasetnames, x and y values to shift pixel coordinates before combining"
+                <param name="coordinates_file" type="data" format="tabular" label="Datasetnames, x and y values to shift pixel coordinates before combining"
             help="Tabular file with three columns: 1 for the filename, 1 for the x-coordinate shift and 1 for the y-coordinate shift. Pixels with the same coordinates after shifting will be deleted."/>
                 <param name="column_x" data_ref="coordinates_file" label="Column with values for shift in x direction" type="data_column"/>
                 <param name="column_y" data_ref="coordinates_file" label="Column with values for shift in y direction" type="data_column"/>
@@ -458,15 +455,21 @@
                 <param name="xy_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
             </when>
         </conditional>
-        <param name="imzml_output" type="boolean" label="Output of imzML file" truevalue="TRUE" falsevalue="FALSE"/>
+        <param name="imzml_output" type="select" display = "radio" optional = "False"
+               label="Output format" help= "Choose the output format">
+                <option value="imzml_format" selected="True">imzML</option>
+                <option value="rdata_format">RData</option>
+        </param>
     </inputs>
     <outputs>
-        <data format="rdata" name="msidata_combined" label="${tool.name} on ${on_string}"/>
+        <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML">
+            <filter>imzml_output=='imzml_format'</filter>
+        </data>
+        <data format="rdata" name="outfile_rdata" label="${tool.name} on ${on_string}: RData">
+            <filter>imzml_output == 'rdata_format'</filter>
+       </data>
         <data format="pdf" name="QC_overview" from_work_dir="Combined_qc.pdf" label = "${tool.name} on ${on_string}: QC"/>
         <data format="tabular" name="pixel_annotations" label="${tool.name} on ${on_string}: annotations"/>
-        <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string} : imzML">
-            <filter>imzml_output</filter>
-       </data>
     </outputs>
     <tests>
         <test>
@@ -481,11 +484,26 @@
             <param name="column_x" value="1"/>
             <param name="column_y" value="2"/>
             <param name="column_names" value="3"/>
+            <param name="imzml_output" value="rdata_format"/>
             <output name="pixel_annotations" file="123_annotation_output.tabular"/>
-            <output name="msidata_combined" file="123_combined.RData" compare="sim_size" />
+            <output name="outfile_rdata" file="123_combined.RData" compare="sim_size" />
             <output name="QC_overview" file="123_combined_QC.pdf" compare="sim_size"/>
         </test>
         <test>
+            <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>
+            <conditional name="annotation_cond">
+                <param name="annotation_tabular" value="no_annotation"/>
+            </conditional>
+            <param name="combine_method" value="automatic_combine"/>
+            <param name="imzml_output" value="imzml_format"/>
+            <output name="QC_overview" file="123_combined_auto.pdf" compare="sim_size"/>
+            <output name="pixel_annotations" file="123_combined_auto.tabular"/>
+            <output name="outfile_imzml" ftype="imzml" file="123_combined_auto.imzml.txt" compare="sim_size">
+                <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="4"/>
+                <extra_files type="file" file="123_combined_auto.ibd" name="ibd" compare="sim_size"/>
+            </output>
+        </test>
+        <test>
             <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>
             <conditional name="annotation_cond">
                 <param name="annotation_tabular" value="annotation"/>
@@ -493,8 +511,9 @@
                 <param name="tabular_header" value="TRUE"/>
             </conditional>
             <param name="combine_method" value="automatic_combine"/>
+            <param name="imzml_output" value="rdata_format"/>
             <output name="pixel_annotations" file="12_annotation_output.tabular"/>
-            <output name="msidata_combined" file="12_combined.RData" compare="sim_size" />
+            <output name="outfile_rdata" file="12_combined.RData" compare="sim_size" />
             <output name="QC_overview" file="12_combined_QC.pdf" compare="sim_size"/>
         </test>
         <test>
@@ -505,9 +524,13 @@
                 <param name="tabular_header" value="TRUE"/>
             </conditional>
             <param name="combine_method" value="automatic_combine"/>
+            <param name="imzml_output" value="imzml_format"/>
             <output name="pixel_annotations" file="112_annotation_output.tabular"/>
-            <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" />
             <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size"/>
+            <output name="outfile_imzml" ftype="imzml" file="112_auto_combined.imzml.txt" compare="sim_size">
+                <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="4"/>
+                <extra_files type="file" file="112_auto_combined.ibd" name="ibd" compare="sim_size"/>
+            </output>
         </test>
         <test>
             <param name="infiles" value="msidata_2.RData,123_combined.RData" ftype="rdata"/>
@@ -515,8 +538,9 @@
                 <param name="annotation_tabular" value="no_annotation"/>
             </conditional>
             <param name="combine_method" value="automatic_combine"/>
+            <param name="imzml_output" value="rdata_format"/>
             <output name="pixel_annotations" file="2123_annotation_output.tabular"/>
-            <output name="msidata_combined" file="2123_auto_combined.RData" compare="sim_size" />
+            <output name="outfile_rdata" file="2123_auto_combined.RData" compare="sim_size" />
             <output name="QC_overview" file="2123_auto_combined_QC.pdf" compare="sim_size"/>
         </test>
     </tests>
@@ -566,9 +590,7 @@
 
 **Output**
 
-- 
-- MSI data as .RData output (can be read with the Cardinal package in R)
-- optional: MSI data as imzML file
+- MSI data as imzML file or .RData (can be read with the Cardinal package in R)
 - pdf that shows the pixel positions and annotations of the combined files
 - Tabular file with pixel annotations (x,y,column with input file names and up to five annotation columns)
 
--- a/macros.xml	Thu Oct 25 07:22:08 2018 -0400
+++ b/macros.xml	Fri Feb 15 10:12:32 2019 -0500
@@ -69,25 +69,92 @@
         ## Range y coordinates
         minimumy = min(coord(msidata)[,2])
         maximumy = max(coord(msidata)[,2])
+
+
+        properties = c("Number of m/z features",
+                       "Range of m/z values",
+                       "Number of pixels", 
+                       "Range of x coordinates", 
+                       "Range of y coordinates")
+
+        values = c(paste0(maxfeatures), 
+                   paste0(minmz, " - ", maxmz), 
+                   paste0(pixelcount), 
+                   paste0(minimumx, " - ", maximumx),
+                   paste0(minimumy, " - ", maximumy))
+
+        property_df = data.frame(properties, values)
+    ]]></token>
+
+    <token name="@READING_MSIDATA_INRAM@"><![CDATA[
+        ## importing MSI data files
+
+        ## function to read RData files independent of filename
+        loadRData <- function(fileName){
+        load(fileName)
+        get(ls()[ls() != "fileName"])
+        }
+
+        #if $infile.ext == 'imzml'
+            #if str($processed_cond.processed_file) == "processed":
+                msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
+                centroided(msidata) = $centroids
+            #else
+                msidata <- readImzML('infile')
+                centroided(msidata) = $centroids
+            #end if
+        #elif $infile.ext == 'analyze75'
+            msidata = readAnalyze('infile')
+            centroided(msidata) = $centroids
+        #else
+            msidata = loadRData('infile.RData')
+        #end if
+
+    ]]></token>
+
+    <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[
+########################### QC numbers ########################
+## including intensity calculations which need data in RAM
+        ## Number of features (mz)
+        maxfeatures = length(features(msidata))
+        ## Range mz
+        minmz = round(min(mz(msidata)), digits=2)
+        maxmz = round(max(mz(msidata)), digits=2)
+        ## Number of spectra (pixels)
+        pixelcount = length(pixels(msidata))
+        ## Range x coordinates
+        minimumx = min(coord(msidata)[,1])
+        maximumx = max(coord(msidata)[,1])
+        ## Range y coordinates
+        minimumy = min(coord(msidata)[,2])
+        maximumy = max(coord(msidata)[,2])
         ## Range of intensities
         minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)
         maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)
         ## Number of intensities > 0, for if conditions
         npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
+        ## Number of NA in spectra matrix
+        NAcount = sum(is.na(spectra(msidata)[]))
+        ## Number of NA in spectra matrix
+        infcount = sum(is.infinite(spectra(msidata)[]))
 
         properties = c("Number of m/z features",
                        "Range of m/z values",
                        "Number of pixels", 
                        "Range of x coordinates", 
                        "Range of y coordinates",
-                       "Range of intensities")
+                       "Range of intensities", 
+                       "Number of NA intensities",
+                       "Number of Inf intensities")
 
         values = c(paste0(maxfeatures), 
                    paste0(minmz, " - ", maxmz), 
                    paste0(pixelcount), 
                    paste0(minimumx, " - ", maximumx),  
                    paste0(minimumy, " - ", maximumy), 
-                   paste0(minint, " - ", maxint))
+                   paste0(minint, " - ", maxint), 
+                   paste0(NAcount), 
+                   paste0(infcount))
 
         property_df = data.frame(properties, values)
     ]]></token>
@@ -144,9 +211,9 @@
     <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
         - Optional file with pixel coordinates and annotation: 
 
-            - Tabular file: One column with x values, one column wiht y values and one column with annotations
+            - Tabular file: One column with x values, one column with y values and one column with annotations
             - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
-            - Pixel with coordinates outside the coordinates of the input file are ignored 
+            - Pixel with coordinates outside the coordinates of the input file are ignored
 
                 ::
 
@@ -161,9 +228,9 @@
 
     <xml name="reading_msidata">
         <param name="infile" type="data" format="imzml,rdata,analyze75"
-               label="Input file as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
-                help="Upload composite datatype imzML (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
-        <param name="centroids" type="boolean" label="Is the input data centroided (picked)" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
+               label="MSI data"
+                help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload)"/>
+        <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
         <conditional name="processed_cond">
             <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
                 <option value="no_processed" selected="True">no</option>
Binary file test-data/112_auto_combined.RData has changed
Binary file test-data/112_auto_combined.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/112_auto_combined.imzml	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,475 @@
+<?xml version="1.0"?>
+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">
+	<cvList count="3">
+		<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />
+		<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />
+		<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />
+	</cvList>
+	<fileDescription>
+		<fileContent>
+			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
+			<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{00A83E55-A8F8-41D4-BBAC-345FA77AAB7E}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9B17E43E3D3B35BE3CD0AE65F40E0C6B27C2752F" />
+			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
+		</fileContent>
+	</fileDescription>
+	<referenceableParamGroupList count="4">
+		<referenceableParamGroup id="spectrum1">
+			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
+			<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />
+			<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="scan1">
+			<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
+			<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="mzArray">
+			<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
+			<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+			<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
+			<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="intensityArray">
+			<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
+			<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
+			<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
+			<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+		</referenceableParamGroup>
+	</referenceableParamGroupList>
+	<sampleList count="1">
+		<sample id="sample1" name="Sample1">
+			<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />
+		</sample>
+	</sampleList>
+	<softwareList count="1">
+		<software id="Cardinal" version="1.12.1">
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+	</softwareList>
+	<scanSettingsList count="1">
+		<scanSettings id="scansettings1">
+			<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="15" />
+			<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
+		</scanSettings>
+	</scanSettingsList>
+	<instrumentConfigurationList count="1">
+		<instrumentConfiguration id="IC1" />
+	</instrumentConfigurationList>
+	<dataProcessingList count="1">
+		<dataProcessing id="CardinalWriteImzML">
+			<processingMethod order="1" softwareRef="Cardinal">
+				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />
+			</processingMethod>
+		</dataProcessing>
+	</dataProcessingList>
+	<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">
+		<spectrumList count="15" defaultDataProcessingRef="CardinalWriteImzML">
+			<spectrum id="Spectrum=1" defaultArrayLength="0" index="1">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="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" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=2" defaultArrayLength="0" index="2">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="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" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=3" defaultArrayLength="0" index="3">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="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" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=4" defaultArrayLength="0" index="4">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="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" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=5" defaultArrayLength="0" index="5">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996" />
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+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=6" defaultArrayLength="0" index="6">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
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+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=7" defaultArrayLength="0" index="7">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<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="33596" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
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+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=8" defaultArrayLength="0" index="8">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
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+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
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+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
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+			</spectrum>
+			<spectrum id="Spectrum=9" defaultArrayLength="0" index="9">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
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+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+					</scan>
+				</scanList>
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/112_auto_combined.imzml.txt	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 556
+-rw-r--r-- 1 meli meli 537552 Feb 12 12:25 ibd
+-rw-r--r-- 1 meli meli  25466 Feb 12 12:25 imzml
Binary file test-data/112_auto_combined_QC.pdf has changed
Binary file test-data/123_annotation.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_annotation.imzml	Fri Feb 15 10:12:32 2019 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_auto_combined.imzml.txt	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 556
+-rw-r--r-- 1 meli meli 537552 Feb 12 12:25 ibd
+-rw-r--r-- 1 meli meli  25466 Feb 12 12:25 imzml
Binary file test-data/123_combined.RData has changed
Binary file test-data/123_combined_QC.pdf has changed
Binary file test-data/123_combined_auto.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined_auto.imzml	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,394 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined_auto.imzml.txt	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
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+-rw-r--r-- 1 meli meli 436764 Feb 12 00:51 ibd
+-rw-r--r-- 1 meli meli  21166 Feb 12 00:51 imzml
Binary file test-data/123_combined_auto.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined_auto.tabular	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,13 @@
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Binary file test-data/12_combined.RData has changed
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Binary file test-data/2123_auto_combined.RData has changed
Binary file test-data/2123_auto_combined_QC.pdf has changed
Binary file test-data/Plot_empty_spectra.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/analyze_filtered.RData has changed
Binary file test-data/analyze_filtered.pdf has changed
Binary file test-data/analyze_filteredoutside.RData has changed
Binary file test-data/analyze_originaloutput.RData has changed
Binary file test-data/analyze_originaloutput2.RData has changed
Binary file test-data/centroids_rdata.pdf has changed
Binary file test-data/cluster_skm.RData has changed
--- a/test-data/features_test2.tabular	Thu Oct 25 07:22:08 2018 -0400
+++ b/test-data/features_test2.tabular	Fri Feb 15 10:12:32 2019 -0500
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--- a/test-data/features_test4.tabular	Thu Oct 25 07:22:08 2018 -0400
+++ b/test-data/features_test4.tabular	Fri Feb 15 10:12:32 2019 -0500
@@ -1,101 +1,101 @@
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--- a/test-data/features_test6.tabular	Thu Oct 25 07:22:08 2018 -0400
+++ b/test-data/features_test6.tabular	Fri Feb 15 10:12:32 2019 -0500
@@ -1,21 +1,21 @@
 mz	r	k	s	classes	centers	tstatistics	p.values	adj.p.values
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 900.50634765625	2	3	2	A	8.5	0	1	1
--- a/test-data/features_test7.tabular	Thu Oct 25 07:22:08 2018 -0400
+++ b/test-data/features_test7.tabular	Fri Feb 15 10:12:32 2019 -0500
@@ -1,101 +1,101 @@
 mz	ncomp	column	coefficients	loadings	weights
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--- a/test-data/loadings_pca.tabular	Thu Oct 25 07:22:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1200 +0,0 @@
-mz	PC1	PC2
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=3" defaultArrayLength="0" index="3">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="7216" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+		</spectrumList>
+	</run>
+</mzML>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out3.imzml.txt	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 24
+-rw-r--r-- 1 meli meli 9616 Feb 12 19:18 ibd
+-rw-r--r-- 1 meli meli 8282 Feb 12 19:18 imzml
Binary file test-data/out4.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out4.imzml	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,205 @@
+<?xml version="1.0"?>
+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">
+	<cvList count="3">
+		<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />
+		<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />
+		<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />
+	</cvList>
+	<fileDescription>
+		<fileContent>
+			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
+			<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{2567A8C4-D2AF-4C81-874C-82E9134A080C}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="EA722C9CF5A229ACF6AEAD177908D73A1C8CB44E" />
+			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
+		</fileContent>
+	</fileDescription>
+	<referenceableParamGroupList count="4">
+		<referenceableParamGroup id="spectrum1">
+			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
+			<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />
+			<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="scan1">
+			<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
+			<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="mzArray">
+			<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
+			<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+			<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
+			<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="intensityArray">
+			<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
+			<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
+			<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
+			<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+		</referenceableParamGroup>
+	</referenceableParamGroupList>
+	<sampleList count="1">
+		<sample id="sample1" name="Sample1">
+			<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />
+		</sample>
+	</sampleList>
+	<softwareList count="1">
+		<software id="Cardinal" version="1.12.1">
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+	</softwareList>
+	<scanSettingsList count="1">
+		<scanSettings id="scansettings1">
+			<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
+			<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
+		</scanSettings>
+	</scanSettingsList>
+	<instrumentConfigurationList count="1">
+		<instrumentConfiguration id="IC1" />
+	</instrumentConfigurationList>
+	<dataProcessingList count="1">
+		<dataProcessing id="CardinalWriteImzML">
+			<processingMethod order="1" softwareRef="Cardinal">
+				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />
+			</processingMethod>
+		</dataProcessing>
+	</dataProcessingList>
+	<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">
+		<spectrumList count="5" defaultDataProcessingRef="CardinalWriteImzML">
+			<spectrum id="Spectrum=1" defaultArrayLength="0" index="1">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4812" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=2" defaultArrayLength="0" index="2">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="9608" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=3" defaultArrayLength="0" index="3">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="14404" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=4" defaultArrayLength="0" index="4">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="19200" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="Spectrum=5" defaultArrayLength="0" index="5">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+					<scan instrumentConfigurationRef="IC1">
+						<referenceableParamGroupRef ref="scan1" />
+						<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="23996" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+		</spectrumList>
+	</run>
+</mzML>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out4.imzml.txt	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 44
+-rw-r--r-- 1 meli meli 28792 Feb 12 00:49 ibd
+-rw-r--r-- 1 meli meli 11141 Feb 12 00:49 imzml
Binary file test-data/out5.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out5.imzml	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,232 @@
+<?xml version="1.0"?>
+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">
+	<cvList count="3">
+		<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />
+		<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />
+		<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />
+	</cvList>
+	<fileDescription>
+		<fileContent>
+			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
+			<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{CC0B2B92-FB40-42C8-822F-834AA528954C}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0B644915E88274BE83FBB110D4CC6D0CDFABAAAC" />
+			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
+		</fileContent>
+	</fileDescription>
+	<referenceableParamGroupList count="4">
+		<referenceableParamGroup id="spectrum1">
+			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
+			<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />
+			<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="scan1">
+			<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
+			<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="mzArray">
+			<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
+			<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+			<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
+			<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+		</referenceableParamGroup>
+		<referenceableParamGroup id="intensityArray">
+			<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
+			<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
+			<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
+			<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+		</referenceableParamGroup>
+	</referenceableParamGroupList>
+	<sampleList count="1">
+		<sample id="sample1" name="Sample1">
+			<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />
+		</sample>
+	</sampleList>
+	<softwareList count="1">
+		<software id="Cardinal" version="1.12.1">
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+	</softwareList>
+	<scanSettingsList count="1">
+		<scanSettings id="scansettings1">
+			<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
+			<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
+		</scanSettings>
+	</scanSettingsList>
+	<instrumentConfigurationList count="1">
+		<instrumentConfiguration id="IC1" />
+	</instrumentConfigurationList>
+	<dataProcessingList count="1">
+		<dataProcessing id="CardinalWriteImzML">
+			<processingMethod order="1" softwareRef="Cardinal">
+				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />
+			</processingMethod>
+		</dataProcessing>
+	</dataProcessingList>
+	<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">
+		<spectrumList count="6" defaultDataProcessingRef="CardinalWriteImzML">
+			<spectrum id="Spectrum=1" defaultArrayLength="0" index="1">
+				<referenceableParamGroupRef ref="spectrum1" />
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
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+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
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+				</scanList>
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
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+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
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+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
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+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
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+				</scanList>
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+</mzML>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out5.imzml.txt	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 20
+-rw-r--r-- 1 meli meli   380 Feb 12 00:50 ibd
+-rw-r--r-- 1 meli meli 12508 Feb 12 00:50 imzml
Binary file test-data/out6.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out6.imzml	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,313 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out6.imzml.txt	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 164
+-rw-r--r-- 1 meli meli 146896 Feb 12 00:51 ibd
+-rw-r--r-- 1 meli meli  16868 Feb 12 00:51 imzml
Binary file test-data/out7.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out7.imzml	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,313 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out7.imzml.txt	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 116
+-rw-r--r-- 1 meli meli 95976 Feb 12 00:51 ibd
+-rw-r--r-- 1 meli meli 16846 Feb 12 00:51 imzml
Binary file test-data/pca_imzml.pdf has changed
--- a/test-data/pixel_out2.tabular	Thu Oct 25 07:22:08 2018 -0400
+++ b/test-data/pixel_out2.tabular	Fri Feb 15 10:12:32 2019 -0500
@@ -1,10 +1,10 @@
-spectra_names	x_values	y_values	pixel_order	peaks_per_spectrum	spectrum_TIC	most_abundant_mz	annotation
-xy_1_1	1	1	1	3672	42479	1267.525390625	col1
-xy_2_1	2	1	2	3672	29179	1264.42407226562	col2
-xy_3_1	3	1	3	3672	37005	1267.525390625	col3
-xy_1_2	1	2	4	3672	42306	1264.38171386719	col1
-xy_2_2	2	2	5	3672	30350	1267.525390625	col2
-xy_3_2	3	2	6	3672	35955	1199.55615234375	col3
-xy_1_3	1	3	7	3672	43872	1199.59753417969	col1
-xy_2_3	2	3	8	3672	33204	1267.48278808594	col2
-xy_3_3	3	3	9	3672	37961	1199.55615234375	col3
+spectra_names	x_values	y_values	pixel_order	peaks_per_spectrum	median_intensity	spectrum_TIC	maximum_intensity	most_abundant_mz	annotation
+xy_1_1	1	1	1	3672	11	42479	43	1267.525390625	col1
+xy_2_1	2	1	2	3672	8	29179	20	1264.42407226562	col2
+xy_3_1	3	1	3	3672	9	37005	42	1267.525390625	col3
+xy_1_2	1	2	4	3672	11	42306	49	1264.38171386719	col1
+xy_2_2	2	2	5	3672	8	30350	21	1267.525390625	col2
+xy_3_2	3	2	6	3672	9	35955	39	1199.55615234375	col3
+xy_1_3	1	3	7	3672	11	43872	84	1199.59753417969	col1
+xy_2_3	2	3	8	3672	9	33204	26	1267.48278808594	col2
+xy_3_3	3	3	9	3672	10	37961	47	1199.55615234375	col3
--- a/test-data/pixel_out3.tabular	Thu Oct 25 07:22:08 2018 -0400
+++ b/test-data/pixel_out3.tabular	Fri Feb 15 10:12:32 2019 -0500
@@ -1,10 +1,10 @@
-spectra_names	x_values	y_values	pixel_order	peaks_per_spectrum	spectrum_TIC	most_abundant_mz	input m/z count
-xy_1_1	1	1	1	241	22.92	329.083343505859	0
-xy_2_1	2	1	2	332	29.26	328.916687011719	0
-xy_3_1	3	1	3	415	24.43	328.916687011719	0
-xy_1_2	1	2	4	343	39.62	329	0
-xy_2_2	2	2	5	301	18.34	328.916687011719	0
-xy_3_2	3	2	6	194	10.79	345.083343505859	0
-xy_1_3	1	3	7	308	14.68	328.916687011719	0
-xy_2_3	2	3	8	367	24.87	329	0
-xy_3_3	3	3	9	323	35.18	329.083343505859	0
+spectra_names	x_values	y_values	pixel_order	peaks_per_spectrum	median_intensity	spectrum_TIC	maximum_intensity	most_abundant_mz	m/z count
+xy_1_1	1	1	1	241	0	22.92	2.48	329.083343505859	0
+xy_2_1	2	1	2	332	0	29.26	2.02	328.916687011719	0
+xy_3_1	3	1	3	415	0	24.43	1.43	328.916687011719	0
+xy_1_2	1	2	4	343	0	39.62	2.59	329	0
+xy_2_2	2	2	5	301	0	18.34	2.38	328.916687011719	0
+xy_3_2	3	2	6	194	0	10.79	1.06	345.083343505859	0
+xy_1_3	1	3	7	308	0	14.68	0.74	328.916687011719	0
+xy_2_3	2	3	8	367	0	24.87	1.33	329	0
+xy_3_3	3	3	9	323	0	35.18	1.73	329.083343505859	0
Binary file test-data/preprocessed.rdata has changed
Binary file test-data/preprocessing_results1.RData has changed
Binary file test-data/preprocessing_results1.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.imzml	Fri Feb 15 10:12:32 2019 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.imzml.txt	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 24
+-rw-r--r-- 1 meli meli    96 Feb 12 21:24 ibd
+-rw-r--r-- 1 meli meli 16714 Feb 12 21:24 imzml
Binary file test-data/preprocessing_results1.pdf has changed
--- a/test-data/preprocessing_results1.txt	Thu Oct 25 07:22:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-mz	x = 1, y = 1	x = 2, y = 1	x = 3, y = 1	x = 1, y = 2	x = 2, y = 2	x = 3, y = 2	x = 1, y = 3	x = 2, y = 3	x = 3, y = 3
-329	8.48069807321137	6.00276368862812	0	0	7.22240715797167	6.68463797360356	0	0	0
-345	0	0	4.70593890744759	0	0	0	5.23000350586712	4.17949067812964	5.08555910047608
Binary file test-data/preprocessing_results2.RData has changed
Binary file test-data/preprocessing_results2.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.imzml	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,394 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.imzml.txt	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 80
+-rw-r--r-- 1 meli meli 54720 Feb 12 21:25 ibd
+-rw-r--r-- 1 meli meli 21132 Feb 12 21:25 imzml
Binary file test-data/preprocessing_results2.pdf has changed
--- a/test-data/preprocessing_results2.txt	Thu Oct 25 07:22:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,297 +0,0 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results4.imzml.txt	Fri Feb 15 10:12:32 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 28
+-rw-r--r-- 1 meli meli  6376 Feb 12 21:29 ibd
+-rw-r--r-- 1 meli meli 16801 Feb 12 21:29 imzml
Binary file test-data/preprocessing_results4.pdf has changed
--- a/test-data/preprocessing_results4.txt	Thu Oct 25 07:22:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,160 +0,0 @@
-mz	x = 1, y = 1	x = 2, y = 1	x = 3, y = 1	x = 1, y = 2	x = 2, y = 2	x = 3, y = 2	x = 1, y = 3	x = 2, y = 3	x = 3, y = 3
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Binary file test-data/preprocessing_results5.RData has changed
Binary file test-data/preprocessing_results5.pdf has changed
--- a/test-data/preprocessing_results5.txt	Thu Oct 25 07:22:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-	x = 1, y = 1	x = 2, y = 1	x = 3, y = 1	x = 1, y = 2	x = 2, y = 2	x = 3, y = 2	x = 1, y = 3	x = 2, y = 3	x = 3, y = 3
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-390	0	0	0	0	0	5.99971986065457e-19	0	2.91871447509579e-26	3.90949821591828e-22
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--- a/test-data/scores_pca.tabular	Thu Oct 25 07:22:08 2018 -0400
+++ b/test-data/scores_pca.tabular	Fri Feb 15 10:12:32 2019 -0500
@@ -1,10 +1,10 @@
 pixel names	x	y	PC1	PC2
-xy_1_1	1	1	1.00970093989579	0.757987492163095
-xy_2_1	2	1	0.579669229309751	-0.365615195586663
-xy_3_1	3	1	-1.04790449059337	0.831141108678224
-xy_1_2	1	2	3.5004093695087	0.608578545994517
-xy_2_2	2	2	-0.325050824762022	0.275854508943195
-xy_3_2	3	2	-1.31374997886227	0.0192699346592569
-xy_1_3	1	3	-1.46193831394872	-0.0337353199555284
-xy_2_3	2	3	-1.08833133183905	1.16461090511219
-xy_3_3	3	3	0.147195401291175	-3.25809198000829
+xy_1_1	1	1	1.009701	0.757987
+xy_2_1	2	1	0.579669	-0.365615
+xy_3_1	3	1	-1.047904	0.831141
+xy_1_2	1	2	3.500409	0.608579
+xy_2_2	2	2	-0.325051	0.275855
+xy_3_2	3	2	-1.31375	0.01927
+xy_1_3	1	3	-1.461938	-0.033735
+xy_2_3	2	3	-1.088331	1.164611
+xy_3_3	3	3	0.147195	-3.258092
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