changeset 2:cbc7e53518ce draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
author galaxyp
date Fri, 15 Feb 2019 10:18:51 -0500
parents 6a03b201bc12
children 585ef27873c9
files classification.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, 4331 insertions(+), 2120 deletions(-) [+]
line wrap: on
line diff
--- a/classification.xml	Thu Oct 25 07:27:07 2018 -0400
+++ b/classification.xml	Fri Feb 15 10:18:51 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="cardinal_classification" name="MSI classification" version="@VERSION@.1">
+<tool id="cardinal_classification" name="MSI classification" version="@VERSION@.2">
     <description>spatial classification of mass spectrometry imaging data</description>
     <macros>
         <import>macros.xml</import>
@@ -28,12 +28,13 @@
 library(lattice)
 library(ggplot2)
 
-@READING_MSIDATA@
+@READING_MSIDATA_INRAM@
 
-## create full matrix to make processed imzML files compatible with classification
-iData(msidata) <- iData(msidata)[] 
+## to make sure that processed files work as well: 
+iData(msidata) = iData(msidata)[]
 
-@DATA_PROPERTIES@
+@DATA_PROPERTIES_INRAM@
+
 
 ######################################## PDF ###################################
 ################################################################################
@@ -60,7 +61,7 @@
 grid.table(property_df, rows= NULL)
 
 
-if (npeaks > 0 && sum(is.na(spectra(msidata)))==0){
+if (npeaks > 0 && sum(is.na(spectra(msidata)[]))==0){
 
     opar <- par()
 
@@ -141,6 +142,10 @@
                 ## PLS-cvApply:
                 msidata.cv.pls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "PLS", ncomp = components)
 
+                ## remove msidata to clean up RAM space
+                rm(msidata)
+                gc()
+
                 ## create table with summary
                 count = 1
                 summary_plscv = list()
@@ -231,9 +236,13 @@
                 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
                 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
 
+                ## remove msidata to clean up RAM space
+                rm(msidata)
+                gc()
                 pls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, pls_classes)
                 colnames(pls_classes2) = c("pixel names", "x", "y","predicted condition")
                 pls_toplabels = topLabels(msidata.pls, n=$type_cond.method_cond.analysis_cond.pls_toplabels)
+                pls_toplabels[,4:6] <-round(pls_toplabels[,4:6],6)
                 write.table(pls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
                 write.table(pls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
 
@@ -275,6 +284,10 @@
                 ## OPLS-cvApply:
                 msidata.cv.opls <- cvApply(msidata, .y = y_vector, .fold = fold_vector, .fun = "OPLS", ncomp = components, keep.Xnew = $type_cond.method_cond.opls_analysis_cond.xnew_cv)
 
+                ## remove msidata to clean up RAM space
+                rm(msidata)
+                gc()
+
                 ## create table with summary
                 count = 1
                 summary_oplscv = list()
@@ -369,7 +382,12 @@
                 opls_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, opls_classes)
                 colnames(opls_classes2) = c("pixel names", "x", "y","predicted condition")
 
+                ## remove msidata to clean up RAM space
+                rm(msidata)
+                gc()
+
                 opls_toplabels = topLabels(msidata.opls, n=$type_cond.method_cond.opls_analysis_cond.opls_toplabels)
+                opls_toplabels[,4:6] <-round(opls_toplabels[,4:6],6)
                 write.table(opls_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
                 write.table(opls_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
 
@@ -410,6 +428,10 @@
                 ## SSC-cvApply:
                 msidata.cv.ssc <- cvApply(msidata, .y = y_vector,.fold = fold_vector,.fun = "spatialShrunkenCentroids", r = c($type_cond.method_cond.ssc_r), s = c($type_cond.method_cond.ssc_s), method = "$type_cond.method_cond.ssc_kernel_method")
 
+                ## remove msidata to clean up RAM space
+                rm(msidata)
+                gc()
+
                 ## create table with summary
                 count = 1
                 summary_ssccv = list()
@@ -502,9 +524,15 @@
                 pixel_names = gsub(" = ", "y_", pixel_names)
                 x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
                 y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
+
+                ## remove msidata to clean up RAM space
+                rm(msidata)
+                gc()
+
                 ssc_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, ssc_classes)
                 colnames(ssc_classes2) = c("pixel names", "x", "y","predicted condition")
                 ssc_toplabels = topLabels(msidata.ssc, n=$type_cond.method_cond.ssc_analysis_cond.ssc_toplabels)
+                ssc_toplabels[,6:9] <-round(ssc_toplabels[,6:9],6)
                 write.table(ssc_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
                 write.table(ssc_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
 
@@ -571,6 +599,11 @@
         predicted_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, predicted_classes)
         colnames(predicted_classes2) = c("pixel names", "x", "y","predicted condition")
         predicted_toplabels = topLabels(prediction, n=$type_cond.predicted_toplabels)
+        if (colnames(predicted_toplabels)[4] == "coefficients"){
+            predicted_toplabels[,4:6] <-round(predicted_toplabels[,4:6],5)
+
+        }else{
+            predicted_toplabels[,6:9] <-round(predicted_toplabels[,6:9],5)}
         write.table(predicted_toplabels, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
         write.table(predicted_classes2, file="$pixeloutput", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
 
@@ -745,7 +778,7 @@
         <param name="output_rdata" type="boolean" label="Results as .RData output" help="Can be used to generate a classification prediction on new data"/>
     </inputs>
     <outputs>
-        <data format="pdf" name="classification_images" from_work_dir="classificationpdf.pdf" label = "${tool.name} on ${on_string}"/>
+        <data format="pdf" name="classification_images" from_work_dir="classificationpdf.pdf" label = "${tool.name} on ${on_string}: results"/>
         <data format="tabular" name="mzfeatures" label="${tool.name} on ${on_string}: features"/>
         <data format="tabular" name="pixeloutput" label="${tool.name} on ${on_string}: pixels"/>
         <data format="rdata" name="classification_rdata" label="${tool.name} on ${on_string}: results.RData">
--- a/macros.xml	Thu Oct 25 07:27:07 2018 -0400
+++ b/macros.xml	Fri Feb 15 10:18:51 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 10:18:51 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">
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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 10:18:51 2019 -0500
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+imzML file:
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+-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
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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 10:18:51 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 10:18:51 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 10:18:51 2019 -0500
@@ -0,0 +1,4 @@
+imzML file:
+total 452
+-rw-r--r-- 1 meli meli 436764 Feb 12 00:51 ibd
+-rw-r--r-- 1 meli meli  21166 Feb 12 00:51 imzml
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 10:18:51 2019 -0500
@@ -0,0 +1,13 @@
+x	y	sample_name
+1	1	msidata_1.RData
+1	2	msidata_1.RData
+1	3	msidata_1.RData
+7	1	msidata_2.RData
+8	1	msidata_2.RData
+7	2	msidata_2.RData
+8	2	msidata_2.RData
+7	3	msidata_2.RData
+8	3	msidata_2.RData
+1	9	msidata_3.RData
+1	10	msidata_3.RData
+1	11	msidata_3.RData
Binary file test-data/12_combined.RData has changed
Binary file test-data/12_combined_QC.pdf has changed
Binary file test-data/2123_auto_combined.RData has changed
Binary file test-data/2123_auto_combined_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 07:27:07 2018 -0400
+++ b/test-data/features_test2.tabular	Fri Feb 15 10:18:51 2019 -0500
@@ -1,101 +1,101 @@
 mz	ncomp	column	coefficients	loadings	weights
-938.823120117188	2	A	0.00557062672565914	0.0521481794011343	0.0618954239030616
-938.859741210938	2	A	0.00542130109915229	0.0573197814782043	0.0556644462038001
-952.817016601562	2	A	0.00540658997062797	0.0541785607809472	0.0556957101293819
-980.9658203125	2	A	0.00530572666388636	0.0640830071706491	0.0596133867741965
-948.876525878906	2	A	0.00513396526933383	0.0580901569940297	0.0501389238916535
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--- a/test-data/features_test4.tabular	Thu Oct 25 07:27:07 2018 -0400
+++ b/test-data/features_test4.tabular	Fri Feb 15 10:18:51 2019 -0500
@@ -1,101 +1,101 @@
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--- a/test-data/features_test6.tabular	Thu Oct 25 07:27:07 2018 -0400
+++ b/test-data/features_test6.tabular	Fri Feb 15 10:18:51 2019 -0500
@@ -1,21 +1,21 @@
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 900.50634765625	2	3	2	A	8.5	0	1	1
--- a/test-data/features_test7.tabular	Thu Oct 25 07:27:07 2018 -0400
+++ b/test-data/features_test7.tabular	Fri Feb 15 10:18:51 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 07:27:07 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1200 +0,0 @@
-mz	PC1	PC2
-300.08	-0.00431122859758329	0.00526403166713949
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-300.25	4.65194150536899e-11	-4.22150087099464e-11
-300.33	1.35108612188122e-11	-1.22607072500498e-11
-300.42	1.05327734584566e-12	-9.55817595104931e-13
-300.5	-8.10333136001904e-07	9.89420809472527e-07
-300.58	-5.81387112967612e-07	7.09876570972713e-07
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Binary file test-data/out3.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out3.imzml	Fri Feb 15 10:18:51 2019 -0500
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+++ b/test-data/out3.imzml.txt	Fri Feb 15 10:18:51 2019 -0500
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+imzML file:
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+-rw-r--r-- 1 meli meli 8282 Feb 12 19:18 imzml
Binary file test-data/out4.ibd has changed
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+					<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 10:18:51 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 10:18:51 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="" />
+					<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="13" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="68" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
+						<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="2" />
+						<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="mzArray" />
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
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+					</binaryDataArray>
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
+						<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="13" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="172" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
+						<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="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" />
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
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+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
+						<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="2" />
+						<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="13" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="276" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
+						<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="3" />
+						<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="13" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
+						<binary />
+					</binaryDataArray>
+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="328" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+		</spectrumList>
+	</run>
+</mzML>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out5.imzml.txt	Fri Feb 15 10:18:51 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 10:18:51 2019 -0500
@@ -0,0 +1,313 @@
+<?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="{24BF18EC-E1DE-4B67-BC12-C3EB475CFC0A}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="DA0417F6AA4EDD71F808B6EA0D7A0706737464EB" />
+			<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="" />
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out6.imzml.txt	Fri Feb 15 10:18:51 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 10:18:51 2019 -0500
@@ -0,0 +1,313 @@
+<?xml version="1.0"?>
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+			</spectrum>
+		</spectrumList>
+	</run>
+</mzML>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out7.imzml.txt	Fri Feb 15 10:18:51 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 07:27:07 2018 -0400
+++ b/test-data/pixel_out2.tabular	Fri Feb 15 10:18:51 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 07:27:07 2018 -0400
+++ b/test-data/pixel_out3.tabular	Fri Feb 15 10:18:51 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 10:18:51 2019 -0500
@@ -0,0 +1,313 @@
+<?xml version="1.0"?>
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+		<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.imzml.txt	Fri Feb 15 10:18:51 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 07:27:07 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
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-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 10:18:51 2019 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+-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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results3.imzml.txt	Fri Feb 15 10:18:51 2019 -0500
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+imzML file:
+total 36
+-rw-r--r-- 1 meli meli 14216 Feb 12 21:26 ibd
+-rw-r--r-- 1 meli meli 16824 Feb 12 21:26 imzml
Binary file test-data/preprocessing_results3.pdf has changed
Binary file test-data/preprocessing_results4.RData has changed
Binary file test-data/preprocessing_results4.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results4.imzml	Fri Feb 15 10:18:51 2019 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results4.imzml.txt	Fri Feb 15 10:18:51 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 07:27:07 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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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 07:27:07 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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Binary file test-data/rdata_notfiltered.RData has changed
Binary file test-data/rdata_notfiltered.pdf has changed
--- a/test-data/scores_pca.tabular	Thu Oct 25 07:27:07 2018 -0400
+++ b/test-data/scores_pca.tabular	Fri Feb 15 10:18:51 2019 -0500
@@ -1,10 +1,10 @@
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Binary file test-data/test2.rdata has changed
Binary file test-data/test3.pdf has changed
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Binary file test-data/test4.rdata has changed
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