changeset 82:8e397b62df4c draft

Uploaded 20171006
author fabio
date Fri, 06 Oct 2017 11:03:56 -0400
parents 6610fd91c760
children f81d72e482cf
files .shed.yml iwtomics-1.0/._.DS_Store iwtomics-1.0/._loadandplot.R iwtomics-1.0/._plotwithscale.R iwtomics-1.0/._testandplot.R iwtomics-1.0/.shed.yml iwtomics-1.0/loadandplot.R iwtomics-1.0/loadandplot.xml iwtomics-1.0/macros.xml iwtomics-1.0/plotwithscale.R iwtomics-1.0/plotwithscale.xml iwtomics-1.0/test-data/._.DS_Store iwtomics-1.0/test-data/input/._Controls_regions.bed iwtomics-1.0/test-data/input/._Elements1_regions.bed iwtomics-1.0/test-data/input/._Elements2_regions.bed iwtomics-1.0/test-data/input/._Elements3_regions.bed iwtomics-1.0/test-data/input/._Feature1.bed iwtomics-1.0/test-data/input/._Feature2.bed iwtomics-1.0/test-data/input/._features.header.bed.txt iwtomics-1.0/test-data/input/._regions.header.txt iwtomics-1.0/test-data/input/Controls_regions.bed iwtomics-1.0/test-data/input/Elements1_regions.bed iwtomics-1.0/test-data/input/Elements2_regions.bed iwtomics-1.0/test-data/input/Elements3_regions.bed iwtomics-1.0/test-data/input/Feature1.bed iwtomics-1.0/test-data/input/Feature2.bed iwtomics-1.0/test-data/input/features.header.bed.txt iwtomics-1.0/test-data/input/regions.header.txt iwtomics-1.0/test-data/output_loadandplot/._iwtomics.loadandplot.RData iwtomics-1.0/test-data/output_loadandplot/._iwtomics.loadandplot.features.txt iwtomics-1.0/test-data/output_loadandplot/._iwtomics.loadandplot.pdf iwtomics-1.0/test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt iwtomics-1.0/test-data/output_loadandplot/iwtomics.loadandplot.RData iwtomics-1.0/test-data/output_loadandplot/iwtomics.loadandplot.features.txt iwtomics-1.0/test-data/output_loadandplot/iwtomics.loadandplot.pdf iwtomics-1.0/test-data/output_loadandplot/iwtomics.loadandplot.regions.txt iwtomics-1.0/test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt iwtomics-1.0/test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf iwtomics-1.0/test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf iwtomics-1.0/test-data/output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt iwtomics-1.0/test-data/output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf iwtomics-1.0/test-data/output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf iwtomics-1.0/test-data/output_testandplot/._iwtomics.testandplot.RData iwtomics-1.0/test-data/output_testandplot/._iwtomics.testandplot.adjustedpvalue.matrix.txt iwtomics-1.0/test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf iwtomics-1.0/test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt iwtomics-1.0/test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf iwtomics-1.0/test-data/output_testandplot/._iwtomics.testandplot.tests.txt iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.RData iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.selectedfeatures.txt iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.summaryplot.pdf iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.tests.txt iwtomics-1.0/testandplot.R iwtomics-1.0/testandplot.xml loadandplot.R loadandplot.xml macros.xml plotwithscale.R plotwithscale.xml test-data/input/Controls_regions.bed test-data/input/Elements1_regions.bed test-data/input/Elements2_regions.bed test-data/input/Elements3_regions.bed test-data/input/Feature1.bed test-data/input/Feature2.bed test-data/input/features.header.bed.txt test-data/input/regions.header.txt test-data/output_loadandplot/iwtomics.loadandplot.RData test-data/output_loadandplot/iwtomics.loadandplot.features.txt test-data/output_loadandplot/iwtomics.loadandplot.pdf test-data/output_loadandplot/iwtomics.loadandplot.regions.txt test-data/output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt test-data/output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf test-data/output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf test-data/output_testandplot/iwtomics.testandplot.RData test-data/output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt test-data/output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf test-data/output_testandplot/iwtomics.testandplot.selectedfeatures.txt test-data/output_testandplot/iwtomics.testandplot.summaryplot.pdf test-data/output_testandplot/iwtomics.testandplot.tests.txt testandplot.R testandplot.xml
diffstat 84 files changed, 12327 insertions(+), 12327 deletions(-) [+]
line wrap: on
line diff
--- a/.shed.yml	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-name: iwtomics
-owner: iuc
-categories:
-  - Statistics
-description: Interval-Wise Testing for Omics Data
-long_description: |
-  Implementation of the Interval-Wise Testing (IWT) for omics data. This
-  inferential procedure tests for differences in "Omics" data between two groups
-  of genomic regions (or between a group of genomic regions and a reference
-  center of symmetry), and does not require fixing location and scale at the
-  outset.
-remote_repository_url: https://github.com/fabio-cumbo/IWTomics4Galaxy
-homepage_url: https://bioconductor.org/packages/release/bioc/html/IWTomics.html
-type: unrestricted
-auto_tool_repositories:
-  name_template: "{{ tool_id }}"
-  descriptor_template: "Wrapper for IWTomics application: {{ tool_name }}."
-suite:
-  name: "suite_iwtomics"
-  description: "A suite of Galaxy tools designed to work with the IWTomics R/Bioconductor package."
-  long_description: |
-    Implementation of the Interval-Wise Testing (IWT) for omics data. This
-    inferential procedure tests for differences in "Omics" data between two groups
-    of genomic regions (or between a group of genomic regions and a reference
-    center of symmetry), and does not require fixing location and scale at the
-    outset.
\ No newline at end of file
Binary file iwtomics-1.0/._.DS_Store has changed
Binary file iwtomics-1.0/._loadandplot.R has changed
Binary file iwtomics-1.0/._plotwithscale.R has changed
Binary file iwtomics-1.0/._testandplot.R has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/.shed.yml	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,26 @@
+name: iwtomics
+owner: iuc
+categories:
+  - Statistics
+description: Interval-Wise Testing for Omics Data
+long_description: |
+  Implementation of the Interval-Wise Testing (IWT) for omics data. This
+  inferential procedure tests for differences in "Omics" data between two groups
+  of genomic regions (or between a group of genomic regions and a reference
+  center of symmetry), and does not require fixing location and scale at the
+  outset.
+remote_repository_url: https://github.com/fabio-cumbo/IWTomics4Galaxy
+homepage_url: https://bioconductor.org/packages/release/bioc/html/IWTomics.html
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  descriptor_template: "Wrapper for IWTomics application: {{ tool_name }}."
+suite:
+  name: "suite_iwtomics"
+  description: "A suite of Galaxy tools designed to work with the IWTomics R/Bioconductor package."
+  long_description: |
+    Implementation of the Interval-Wise Testing (IWT) for omics data. This
+    inferential procedure tests for differences in "Omics" data between two groups
+    of genomic regions (or between a group of genomic regions and a reference
+    center of symmetry), and does not require fixing location and scale at the
+    outset.
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/loadandplot.R	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,144 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+  args=commandArgs(TRUE)
+  
+  # get args names and values
+  args_values=strsplit(args,'=')
+  args_names=unlist(lapply(args_values,function(arg) arg[1]))
+  names(args_values)=args_names
+  args_values=lapply(args_values,function(arg) arg[2])
+  # read filenames
+  outrdata=args_values$outrdata
+  outregions=args_values$outregions
+  outfeatures=args_values$outfeatures
+  outpdf=args_values$outpdf
+  regionspaths=unlist(strsplit(args_values$regionspaths,'\\|'))
+  if("regionsheaderfile" %in% args_names){
+    # the file regionsheaderfile must contain as first column the (unique) regionsfilenames, 
+    # as second column the corresponding ids and as third column the names
+    tryCatch({
+      regionsheader=read.delim(args_values$regionsheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
+      regionsfilenames=unlist(strsplit(args_values$regionsfilenames,'\\|'))
+      if(length(setdiff(regionsfilenames,row.names(regionsheader)))) {
+        write("IWTomics message: Not all region files are present in the first column of header file for regions.", stderr())
+        quit(save="no", status=11)
+      }
+      id_regions=regionsheader[regionsfilenames,1]
+      name_regions=regionsheader[regionsfilenames,2]
+    }, error = function(err) {
+      write("IWTomics message: An error has occurred reading the header file for regions. Please try again.", stderr())
+      quit(save="no", status=10) #error on header file
+    })
+  }else{
+    eval(parse(text=args[[which(args_names=='regionsgalaxyids')]]))
+    id_regions=paste0('data_',regionsgalaxyids)
+    name_regions=paste0('data_',regionsgalaxyids)
+  }
+  featurespaths=unlist(strsplit(args_values$featurespaths,'\\|'))
+  if("featuresheaderfile" %in% args_names){
+    # the file featuresheaderfile must contain as first column the (unique) featuresfilenames, 
+    # as second column the corresponding ids and as third column the names
+    tryCatch({
+      featuresheader=read.delim(args_values$featuresheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
+      featuresfilenames=unlist(strsplit(args_values$featuresfilenames,'\\|'))
+      if(length(setdiff(featuresfilenames,row.names(featuresheader)))) {
+        write("IWTomics message: Not all feature files are present in the first column of header file for features.", stderr())
+        quit(save="no", status=21)
+      }
+      id_features=featuresheader[featuresfilenames,1]
+      name_features=featuresheader[featuresfilenames,2]
+    }, error = function(err) {
+      write("IWTomics message: An error has occurred reading the header file for features. Please try again.", stderr())
+      quit(save="no", status=20) #error on header file
+    })
+  }else{
+    eval(parse(text=args[[which(args_names=='featuresgalaxyids')]]))
+    id_features=paste0('data_',featuresgalaxyids)
+    name_features=paste0('data_',featuresgalaxyids)
+  }
+  # read parameters (from smoothing on)
+  i_smoothing=which(args_names=='smoothing')
+  for(i in i_smoothing:length(args)){
+    eval(parse(text=args[[i]]))
+  }
+  
+  # load data
+  tryCatch({
+    regionsFeatures=IWTomicsData(regionspaths,featurespaths,alignment,
+                                id_regions,name_regions,id_features,name_features,start.are.0based=start.are.0based)
+  }, error = function(err) {
+    if(grepl('invalid format',err$message)){
+      write("IWTomics message: Not enough columns in input file.", stderr())
+      quit(save="no", status=31) # error, not enough columns in input file
+    }else if(grepl('duplicated regions',err$message)){
+      write("IWTomics message: Duplicated regions in region file.", stderr())
+      quit(save="no", status=32) # error, duplicated regions in region file
+    }else if(grepl('duplicated windows',err$message)){
+      write("IWTomics message: Duplicated windows in feature file.", stderr())
+      quit(save="no", status=33) # error, duplicated windows in feature file
+    }else if(grepl('overlapping windows',err$message)){
+      write("IWTomics message: Overlapping windows in feature file.", stderr())
+      quit(save="no", status=34) # error, overlapping windows in feature file
+    }else if(grepl('not all regions in datasets',err$message)){
+      write("IWTomics message: Windows in feature files do not cover all regions in region files.", stderr())
+      quit(save="no", status=35) # error, windows in feature files do not cover all regions in region files
+    }else if(grepl('ifferent size windows',err$message)){
+      write("IWTomics message: All windows in a feature file must have the same size.", stderr())
+      quit(save="no", status=36) # error, all windows in a feature files must have the same size
+    }
+    #error loading data
+    write("IWTomics message: An error has occurred reading the data. Please try again.", stderr())
+    quit(save="no", status=30)    
+ })
+  
+  # smooth data
+  if(smoothing!='no'){
+    tryCatch({
+      if(smoothing=='locpoly'){
+        dist_knots=10
+      }else if(smoothing=='kernel'){
+        degree=3
+        dist_knots=10
+      }else if(smoothing=='splines'){
+        bandwidth=5
+      }
+      if(alignment=='scale'){
+        if(scale==0){
+          regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+                                bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
+        }else{
+          regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+                                bandwidth=bandwidth,degree=degree,dist_knots=dist_knots,scale_grid=scale)
+        }
+      }else{
+        regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+                              bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
+      }
+    }, error = function(err) {
+      write("IWTomics message: An error has occurred smoothing the data. Please try again.", stderr())
+      quit(save="no", status=40) #error on smoothing
+    })
+  }
+  
+  # plot data
+  pdf(outpdf,width=10,height=8)
+  if(plottype=='boxplot'){
+    # fix repeated probs
+    probs=sort(unique(probs))
+  }else{
+    probs=c(0.25,0.5,0.75)
+  }
+  plot(regionsFeatures,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
+  dev.off()
+  
+  # create output
+  #write.table(cbind(unlist(strsplit(args_values$regionsfilenames,'\\|')),idRegions(regionsFeatures),nameRegions(regionsFeatures)),
+              #file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  write.table(as.data.frame(t(idRegions(regionsFeatures))),file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  #write.table(cbind(unlist(strsplit(args_values$featuresfilenames,'\\|')),idFeatures(regionsFeatures),nameFeatures(regionsFeatures)),
+              #file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  write.table(as.data.frame(t(idFeatures(regionsFeatures))),file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  save(regionsFeatures,file=outrdata)
+}else{
+  write("IWTomics message: Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
+  quit(save="no", status=255)
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/loadandplot.xml	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,237 @@
+<tool id="iwtomics_loadandplot" name="IWTomics Load" version="@VERSION@.0">
+  <description>Smooth and Plot</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+
+  <command detect_errors="exit_code">
+<![CDATA[
+    Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
+
+      #set region_paths = '|'.join( [ str( $r ) for $r in $regions ] )
+      regionspaths='${region_paths}'
+      #set region_galaxyids = ','.join( [ str( $r.hid ) for $r in $regions ] )
+      regionsgalaxyids='c(${region_galaxyids})'
+      #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] )
+      regionsfilenames='${region_names}'
+      #set region_header = str( $regionsheader )
+      #if $region_header != "None":
+        regionsheaderfile='${region_header}'
+      #end if
+      
+      #set feature_paths = '|'.join( [ str( $f ) for $f in $features ] )
+      featurespaths='${feature_paths}'
+      #set feature_galaxyids = ','.join( [ str( $f.hid ) for $f in $features ] )
+      featuresgalaxyids='c(${feature_galaxyids})'
+      #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] )
+      featuresfilenames='${feature_names}'
+      #set feature_header = str( $featuresheader )
+      #if $feature_header != "None":
+        featuresheaderfile='${feature_header}'
+      #end if
+
+      smoothing="'${conditionaltype.smoothing}'"
+      start.are.0based='${zerobased}'
+      #if $conditionaltype.smoothing == 'no':
+        alignment="'${conditionaltype.alignment}'"
+      #elif $conditionaltype.smoothing == 'locpoly':
+        bandwidth='${conditionaltype.locpolybandwidth}'
+        degree='${conditionaltype.locpolydegree}'
+        alignment="'${conditionaltype.conditionalscale.alignment}'"
+      #elif $conditionaltype.smoothing == 'kernel':
+        bandwidth='${conditionaltype.kernelbandwidth}'
+        alignment="'${conditionaltype.conditionalscale.alignment}'"
+      #elif $conditionaltype.smoothing == 'splines':
+        degree='${conditionaltype.splinesdegree}'
+        dist_knots='${conditionaltype.splinesdistknots}'
+        alignment="'${conditionaltype.conditionalscale.alignment}'"
+      #end if
+
+      #if $conditionaltype.smoothing != 'no':
+        #if $conditionaltype.conditionalscale.alignment == 'scale':
+          scale='${conditionaltype.conditionalscale.scalegrid}'
+          fill_gaps='TRUE'
+        #else
+          fill_gaps='${conditionaltype.conditionalscale.fillgaps}'
+        #end if
+      #end if
+
+      average='${plotres.average}'
+      size='${plotres.size}'
+      plottype="'${plotres.conditionalplottype.plottype}'"
+      #if $plotres.conditionalplottype.plottype == 'boxplot':
+        #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #if $probs != "":
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
+        #else:
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
+        #end if
+      #end if      
+]]>
+  </command>
+
+  <inputs>
+    <!-- regions -->
+    <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
+    <param format="tabular" name="regionsheader" type="data" label="Insert header file for regions (optional)" optional="true" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output." />
+
+    <!-- features -->
+    <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" />
+    <param format="tabular" name="featuresheader" type="data" label="Insert header file for features (optional)" optional="true" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output." />
+
+    <!-- zero-base one-base -->
+    <param name="zerobased" type="select" label="Start positions are:" multiple="false" help="">
+      <option value="TRUE">0-based</option>
+      <option value="FALSE">1-based</option>
+    </param>
+
+    <!-- conditional smoothing -->
+    <conditional name="conditionaltype">
+      <!-- smoothing -->
+      <param name="smoothing" type="select" label="Smoothing" help="Type of smoothing to be applied to the feature curves.">
+        <option value="no">No</option>
+        <option value="locpoly">Local Polynomials</option>
+        <option value="kernel">Gaussian Kernel</option>
+        <option value="splines">B-Splines</option>
+      </param>
+      <!-- conditional choice: smoothing=no -->
+      <when value="no">
+        <expand macro="alignment" />
+      </when>
+      <!-- conditional choice: smoothing=locpoly -->
+      <when value="locpoly">
+        <param name="locpolybandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
+        <param name="locpolydegree" type="integer" value="3" min="0" label="Degree of local polynomial" help="" />
+        <!-- conditional region alignment -->
+        <expand macro="alignment-s" />
+      </when>
+      <!-- conditional choice: smoothing=kernel -->
+      <when value="kernel">
+        <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
+        <!-- conditional region alignment -->
+        <expand macro="alignment-s" />
+      </when>
+      <!-- conditional choice: smoothing=splines -->
+      <when value="splines">
+        <param name="splinesdegree" type="integer" value="3" min="0" label="Degree of B-splines" help="" />
+        <param name="splinesdistknots" type="integer" value="10" min="2" label="Distance between nodes (approximate)" help="" />
+        <!-- conditional region alignment -->
+        <expand macro="alignment-s" />
+      </when>
+    </conditional>
+
+    <!-- plot IWTomics results -->
+    <section name="plotres" title="Plot data" expanded="True">
+      <expand macro="plot-params" />
+    </section>
+  </inputs>
+
+  <outputs>
+    <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" />
+    <data format="tabular" name="outregions" label="${tool.name} on ${on_string}: Region Dataset IDs" from_work_dir="iwtomics.loadandplot.regions.txt" />
+    <data format="tabular" name="outfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.loadandplot.features.txt" />
+    <data format="pdf" name="outpdf" label="${tool.name} on ${on_string}: Plotted Data" from_work_dir="iwtomics.loadandplot.pdf" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="regions" value="input/Controls_regions.bed,input/Elements1_regions.bed,input/Elements2_regions.bed,input/Elements3_regions.bed" ftype="bed" />
+      <param name="regionsheader" value="input/regions.header.txt" ftype="tabular" />
+      <param name="features" value="input/Feature1.bed,input/Feature2.bed" ftype="bed" />
+      <param name="featuresheader" value="input/features.header.bed.txt" ftype="tabular" />
+      <param name="zerobased" value="TRUE" />
+      <param name="smoothing" value="kernel" />
+      <param name="alignment" value="center" />
+      <param name="kernelbandwidth" value="5" />
+      <param name="fillgaps" value="TRUE" />
+      <param name="average" value="TRUE" />
+      <param name="size" value="TRUE" />
+      <param name="plottype" value="boxplot" />
+      <param name="prob0" value="0.25" />
+      <param name="prob1" value="0.5" />
+      <param name="prob2" value="0.75" />
+      <output name="outrdata" file="output_loadandplot/iwtomics.loadandplot.RData" compare="sim_size" />
+      <output name="outregions" file="output_loadandplot/iwtomics.loadandplot.regions.txt" />
+      <output name="outfeatures" file="output_loadandplot/iwtomics.loadandplot.features.txt" />
+      <output name="outpdf" file="output_loadandplot/iwtomics.loadandplot.pdf" compare="sim_size" />
+    </test>
+  </tests>
+
+  <help><![CDATA[
+This tool imports a collection of genomic region datasets, and associates to each region
+multiple genomic feature measurements. It allows to align the regions in multiple ways
+(center, left, right or scale alignment), to smooth the feature curves (possibly filling gaps in the
+measurements) and to create a graphical representation of the feature measurements in each
+region datasets (aligned curves or pointwise quantile curves).
+
+-----
+
+**Region datasets**
+
+Each region dataset can be provided as a BED or Tabular file with tab delimited columns chr
+start end (extra columns present in the input file are ignored). Regions can be of different
+length::
+
+    chr2  49960150  50060150
+    chr2  55912445  56012445
+    ...
+
+-----
+
+**Feature measurements**
+
+Feature measurements corresponding to all the regions can be provided as a BED or Tabular
+file with tab delimited columns chr start end value::
+
+    chr2  49960150  49962150  0.9426
+    chr2  49962150  49964150  0.7816
+    ...
+
+Each feature must be measured in windows of a fixed size inside all the regions (missing
+values must be indicated as NA). Another way to import feature measurements is from a
+Tabular file with the first three columns chr start end corresponding to the different genomic
+regions, followed on the same row by all the measurements in fixed-size windows::
+
+    chr2  49960150  50060150  0.9426  0.7816  0.8921  ...  ...  1.2063
+    chr2  55912445  56012445  0.8719  0.9975  1.1619  ...  ...  0.9601
+    ...
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. RData with the IWTomicsData object, that stores the aligned genomic region datasets, and their associated feature measurements;
+2. Region dataset identifiers;
+3. Feature identifiers;
+4. PDF file with the plotted data.
+
+1-3 can be used as input of the tool *IWTomics Test and Plot*
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy - fabio.cumbo@iasi.cnr.it) and Marzia A. Cremona (The Pennsylvania State University, USA - mac78@psu.edu).
+
+It implements a simplified version of the methods *smooth* and *plot* for *IWTomicsData* objects.
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+
+Example data can be found at:
+
+1. Simulated_data_
+2. ETn_data_
+
+.. _Simulated_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-example
+.. _ETn_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-etn-example
+  ]]></help>
+
+  <expand macro="citations" />
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/macros.xml	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,106 @@
+<macros>
+    <token name="@VERSION@">1.0.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.3.1">r-base</requirement>
+            <requirement type="package" version="@VERSION@">bioconductor-iwtomics</requirement>
+        </requirements>
+    </xml>
+    
+    <xml name="alignment-s">
+        <conditional name="conditionalscale">
+            <param name="alignment" type="select" label="Region alignment" help="">
+                <option value="center">Center - Alignment on the central position</option>
+                <option value="left">Left - Alignment on the starting position</option>
+                <option value="right">Right - Alignment on the ending position</option>
+                <option value="scale">Scale - Scaling all regions to the same length</option>
+            </param>
+            <when value="center">
+                <!-- fill gaps -->
+                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+            </when>
+            <when value="left">
+                <!-- fill gaps -->
+                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+            </when>
+            <when value="right">
+                <!-- fill gaps -->
+                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+            </when>
+            <when value="scale">
+                <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="alignment">
+        <param name="alignment" type="select" label="Region alignment" help="">
+            <option value="center">Center - Alignment on the central position</option>
+            <option value="left">Left - Alignment on the starting position</option>
+            <option value="right">Right - Alignment on the ending position</option>
+        </param>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1080/10485252.2017.1306627</citation>
+            <citation type="bibtex">
+                @MANUAL{
+                        iwtomics,
+                        author = {Cremona, M.A. and Pini, A. and Chiaromonte, F. and Vantini, S.},
+                        title = {IWTomics: Interval-Wise Testing for Omics Data},
+                        note = {R package version 1.0.0},
+                        year = {2017}
+                }
+            </citation>
+        </citations>
+    </xml>
+
+    <xml name="plot-params">
+        <!-- average -->
+        <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
+        <!-- average -->
+        <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
+        <!-- conditional plot type -->
+        <conditional name="conditionalplottype">
+            <!-- plot type -->
+            <param name="plottype" type="select" label="Plot type">
+            <option value="boxplot">Pointwise quantile curves (boxplot)</option>
+            <option value="curves">Curves (aligned)</option>
+            </param>
+            <!-- conditional choice: plottype=boxplot -->
+            <when value="boxplot">
+            <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
+                <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
+                <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+                <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
+                <repeat name="probabilities" title="Probabilities">
+                <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+                </repeat>
+            </section>
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="plot-sum">
+        <section name="plotsum" title="Summary plot" expanded="True">
+            <!-- conditional group by -->
+            <conditional name="conditionalgroupby">
+                <!-- group by -->
+                <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
+                <option value="none">No plot</option>
+                <option value="test">Group by test</option>
+                <option value="feature">Group by feature</option>
+                </param>
+                <when value="test">
+                <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+                <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+                </when>
+                <when value="feature">
+                <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+                <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+                </when>
+            </conditional>
+        </section>
+    </xml>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/plotwithscale.R	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,117 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+  args=commandArgs(TRUE)
+  
+  # get args names and values
+  args_values=strsplit(args,'=')
+  args_names=unlist(lapply(args_values,function(arg) arg[1]))
+  names(args_values)=args_names
+  args_values=lapply(args_values,function(arg) arg[2])
+  # read filenames
+  adjustedpvalue=args_values$adjustedpvalue
+  iwtomicsrespdf=args_values$iwtomicsrespdf
+  iwtomicssumpdf=args_values$iwtomicssumpdf
+  iwtomicsrdata=args_values$iwtomicsrdata
+  iwtomicstests=args_values$iwtomicstests
+  iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
+  test_subset=paste0('c(',strsplit(args_values$test_subset,'\\|')[[1]],')')
+  feature_subset=paste0('c(',strsplit(args_values$feature_subset,'\\|')[[1]],')')
+  # read parameters (from test_subset on)
+  i_scale_subset=which(args_names=='scale_subset')
+  for(i in i_scale_subset:length(args)){
+    eval(parse(text=args[[i]]))
+  }
+  
+  # load RData
+  load(iwtomicsrdata)
+  # read testids and featureids and check them
+  unlisted=lapply(seq_along(test_subset),
+                   function(i){
+                     test_subset_i=eval(parse(text=test_subset[i]))
+                     feature_subset_i=eval(parse(text=feature_subset[i]))
+                     test_subset_i=rep(test_subset_i,each=length(feature_subset_i))
+                     feature_subset_i=rep(feature_subset_i,length.out=length(test_subset_i))
+                     scale_subset_i=rep(scale_subset[i],length(test_subset_i))
+                     return(list(test_subset=test_subset_i,feature_subset=feature_subset_i,scale_subset=scale_subset_i))
+                   })
+  test_subset=unlist(lapply(unlisted,function(l) l$test_subset))
+  feature_subset=unlist(lapply(unlisted,function(l) l$feature_subset))
+  scale_subset=unlist(lapply(unlisted,function(l) l$scale_subset))
+  testids=as.character(read.delim(iwtomicstests,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  featureids=as.character(read.delim(iwtomicsselectedfeatures,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  id_features_subset=featureids[feature_subset]
+  if(sum(testids!=paste(testInput(regionsFeatures_test)$id_region1,'vs',testInput(regionsFeatures_test)$id_region2))){
+    write("Wrong test ids.", stderr())
+    quit(save="no", status=10)
+  }
+  if(sum(featureids!=idFeatures(regionsFeatures_test))){
+    write("Wrong feature ids.", stderr())
+    quit(save="no", status=20)
+  }
+  # retrieve test and features_subset ids
+  id_features_subset=featureids[feature_subset]
+  if(sum(duplicated(paste0(test_subset,id_features_subset)))){
+    write("Two scale thresholds selected for the same test and feature.", stderr())
+    quit(save="no", status=30)
+  }
+  # If scale_subset=0, do not change the threshold
+  default=(scale_subset==0)
+  scale_subset=scale_subset[!default]
+  test_subset=test_subset[!default]
+  id_features_subset=id_features_subset[!default]
+  
+  # get scale threshold
+  scale_threshold=lapply(regionsFeatures_test@test$result,
+                         function(result) unlist(lapply(result,function(feature) feature$max_scale)))
+  for(i in seq_along(test_subset)){
+    if(scale_threshold[[test_subset[i]]][id_features_subset[i]]<scale_subset[i]){
+      write("Scale threshold too high.", stderr())
+      quit(save="no", status=40)
+    }
+    scale_threshold[[test_subset[i]]][id_features_subset[i]]=scale_subset[i]
+  }
+  
+  # create adjustedvalue output
+  pval=adjusted_pval(regionsFeatures_test,scale_threshold=scale_threshold)
+  for(test in seq_along(pval)){
+    for(id_feature in idFeatures(regionsFeatures_test)){
+      write(paste0('Test: ',testids[test],', on feature ',id_feature),
+              file=adjustedpvalue,append=TRUE,sep='\t')
+        pval_i=as.data.frame(t(pval[[test]][[id_feature]]))
+        row.names(pval_i)=paste('Scale',scale_threshold[[test]][[id_feature]])
+        write.table(pval_i,file=adjustedpvalue,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
+        write('',file=adjustedpvalue,append=TRUE,sep='\t')
+      }
+    }
+  
+  
+  # plot test results
+  pdf(iwtomicsrespdf,width=5,height=7)
+  if(plottype=='boxplot'){
+    # fix repeated probs
+    probs=sort(unique(probs))
+  }else{
+    probs=c(0.25,0.5,0.75)
+  }
+  plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,scale_threshold=scale_threshold,ask=FALSE)
+  dev.off()
+  
+  # plot summary results
+  if(groupby!='none'){
+    tryCatch({
+      pdf(iwtomicssumpdf,width=15,height=10)
+      plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,scale_threshold=scale_threshold,ask=FALSE,append=TRUE)
+      dev.off()
+    }, error = function(err) {
+      if (grepl('selected features with different resolution',err$message)) {
+        write("Group by 'test' but selected features with different resolution.", stderr())
+        quit(save="no", status=50) #error: groupby 'test' but selected features with different resolution.
+      }
+      write("Summary plot error. Please try again.", stderr())
+      quit(save="no", status=60) #error 
+    })
+  }
+  
+}else{
+  write("Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
+  quit(save="no", status=255)
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/plotwithscale.xml	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,149 @@
+<tool id="iwtomics_plotwithscale" name="IWTomics Plot with Threshold" version="@VERSION@.0">
+  <description>on Test Scale</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  
+  <command detect_errors="exit_code">
+<![CDATA[
+    Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
+      iwtomicsrdata='${rdata}'
+      iwtomicstests='${testids}'
+      iwtomicsselectedfeatures='${featureids}'
+
+      #set test_subset = '|'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
+      test_subset='${test_subset}'
+      #set feature_subset = '|'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
+      feature_subset='${feature_subset}'
+      #set scale_subset = ','.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
+      scale_subset='c(${scale_subset})'
+
+      testalpha='${plotres.alpha}'
+      average='${plotres.average}'
+      size='${plotres.size}'
+      plottype="'${plotres.conditionalplottype.plottype}'"
+      #if $plotres.conditionalplottype.plottype == 'boxplot':
+        #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #if $probs != "":
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
+        #else:
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
+        #end if
+      #end if
+
+      groupby="'${plotsum.conditionalgroupby.groupby}'"
+      #if $plotsum.conditionalgroupby.groupby == "test":
+        summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
+        only_significant='${plotsum.conditionalgroupby.testonlysig}'
+      #elif $plotsum.conditionalgroupby.groupby == "feature":
+        summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
+        only_significant='${plotsum.conditionalgroupby.featureonlysig}'
+      #end if
+]]>
+  </command>
+
+  <inputs>
+    <!-- RData -->
+    <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object with test results" help="File created by 'IWTomics Test and Plot'." />
+    <!-- test IDs -->
+    <param format="tabular" name="testids" type="data" label="Select test IDs" help="File created by 'IWTomics Test and Plot'." />
+    <!-- feature IDs -->
+    <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Test and Plot'." />
+
+    <!-- repeat threshold on test scale -->
+    <section name="scalesection" title="Select scale for Interval-Wise Testing and plot" expanded="True" help="Maximum interval length for the p-value adjustment. If 0 the maximum possible scale is used.">
+      <repeat name="thresholdontestscale" title="Threshold on test scale" min="1">
+        <param name="test" type="data_column" data_ref="testids" numerical="False" label="Test ID" multiple="True" use_header_names="True" />
+        <param name="feature" type="data_column" data_ref="featureids" numerical="False" label="Feature ID" multiple="True" use_header_names="True" />
+        <param name="scale" type="integer" value="0" min="0" label="Scale" />
+      </repeat>
+    </section>
+
+    <!-- plot IWTomics results -->
+    <section name="plotres" title="Plot IWTomics test results" expanded="True">
+      <!-- alpha -->
+      <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+      <expand macro="plot-params" />
+    </section>
+
+    <!-- summary plot -->
+    <expand macro="plot-sum" />
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" />
+    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" />
+    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="rdata" value="output_testandplot/iwtomics.testandplot.RData" ftype="rdata" />
+      <param name="testids" value="output_testandplot/iwtomics.testandplot.tests.txt" ftype="tabular" />
+      <param name="featureids" value="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" ftype="tabular" />
+      <repeat name="thresholdontestscale">
+        <param name="test" value="1" />
+        <param name="feature" value="1" />
+        <param name="scale" value="10" />
+      </repeat>
+      <repeat name="thresholdontestscale">
+        <param name="test" value="1,2,3" />
+        <param name="feature" value="2" />
+        <param name="scale" value="20" />
+      </repeat>
+      <param name="alpha" value="0.05" />
+      <param name="average" value="TRUE" />
+      <param name="size" value="TRUE" />
+      <param name="plottype" value="boxplot" />
+      <param name="prob0" value="0.25" />
+      <param name="prob1" value="0.5" />
+      <param name="prob2" value="0.75" />
+      <param name="groupby" value="feature" />
+      <param name="featurealphaplot" value="0.05" />
+      <param name="featureonlysig" value="TRUE" />
+      <output name="adjustedpvalue" file="output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt" compare="sim_size" />
+      <output name="iwtomicsrespdf" file="output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf" compare="sim_size" />
+      <output name="iwtomicssumpdf" file="output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf" compare="sim_size" />
+    </test>
+  </tests>
+
+  <help><![CDATA[
+This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
+for the different tests performed at the selected scale, and it creates a graphical representation of the
+Interval-Wise Testing results and a summary plot (optional) at the selected scale.
+
+-----
+
+**Input files**
+
+RData file with the IWTomicsData object with test results, tabular files with test IDs and feature IDs.
+These files are created by the tool *IWTomics Test and Plot*.
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. TXT file with an adjusted p-value curve for every test performed at the selected scale;
+2. PDF file with the plotted test results;
+3. PDF file with the summary plot.
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+  ]]></help>
+
+  <expand macro="citations" />
+
+</tool>
Binary file iwtomics-1.0/test-data/._.DS_Store has changed
Binary file iwtomics-1.0/test-data/input/._Controls_regions.bed has changed
Binary file iwtomics-1.0/test-data/input/._Elements1_regions.bed has changed
Binary file iwtomics-1.0/test-data/input/._Elements2_regions.bed has changed
Binary file iwtomics-1.0/test-data/input/._Elements3_regions.bed has changed
Binary file iwtomics-1.0/test-data/input/._Feature1.bed has changed
Binary file iwtomics-1.0/test-data/input/._Feature2.bed has changed
Binary file iwtomics-1.0/test-data/input/._features.header.bed.txt has changed
Binary file iwtomics-1.0/test-data/input/._regions.header.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/input/Controls_regions.bed	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,35 @@
+chr1	91399892	91499892
+chr1	116447079	116547079
+chr2	231381109	231481109
+chr3	47386633	47486633
+chr3	99195712	99295712
+chr3	116765114	116865114
+chr3	134345017	134445017
+chr4	68064019	68164019
+chr4	137465811	137565811
+chr4	173293016	173393016
+chr5	59044110	59144110
+chr5	94592763	94692763
+chr5	108436006	108536006
+chr5	110836898	110936898
+chr5	146661073	146761073
+chr6	99727306	99827306
+chr7	88291325	88391325
+chr7	120999784	121099784
+chr8	126860366	126960366
+chr8	127636547	127736547
+chr11	41362564	41462564
+chr11	101741527	101841527
+chr12	15210277	15310277
+chr13	91106037	91206037
+chr13	91518822	91618822
+chr13	98959030	99059030
+chr15	39087176	39187176
+chr17	58542142	58642142
+chr18	12199823	12299823
+chr20	8173704	8273704
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/input/Elements1_regions.bed	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,25 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/input/Elements2_regions.bed	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,20 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/input/Elements3_regions.bed	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,28 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/input/Feature1.bed	Fri Oct 06 11:03:56 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/input/Feature2.bed	Fri Oct 06 11:03:56 2017 -0400
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+chr21	16064609	16066609	6.11742019669001
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/input/features.header.bed.txt	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,2 @@
+Feature1.bed	ftr1	Feature 1
+Feature2.bed	ftr2	Feature 2
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/input/regions.header.txt	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,4 @@
+Elements1_regions.bed	elem1	Elements 1
+Elements2_regions.bed	elem2	Elements 2
+Elements3_regions.bed	elem3	Elements 3
+Controls_regions.bed	control	Controls
\ No newline at end of file
Binary file iwtomics-1.0/test-data/output_loadandplot/._iwtomics.loadandplot.RData has changed
Binary file iwtomics-1.0/test-data/output_loadandplot/._iwtomics.loadandplot.features.txt has changed
Binary file iwtomics-1.0/test-data/output_loadandplot/._iwtomics.loadandplot.pdf has changed
Binary file iwtomics-1.0/test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt has changed
Binary file iwtomics-1.0/test-data/output_loadandplot/iwtomics.loadandplot.RData has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/output_loadandplot/iwtomics.loadandplot.features.txt	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,1 @@
+ftr1	ftr2
Binary file iwtomics-1.0/test-data/output_loadandplot/iwtomics.loadandplot.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/output_loadandplot/iwtomics.loadandplot.regions.txt	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,1 @@
+control	elem1	elem2	elem3
Binary file iwtomics-1.0/test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt has changed
Binary file iwtomics-1.0/test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf has changed
Binary file iwtomics-1.0/test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,18 @@
+Test: elem1 vs control, on feature ftr1
+Scale 10	0.337	0.492	0.718	0.884	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.886	0.817	0.813	0.839	0.889	0.947	0.983	0.97	0.97	0.935	0.777	0.554	0.362	0.457	0.681	0.84	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.852	0.752	0.691	0.802	0.905	0.995	0.995	0.937	0.817	0.688
+
+Test: elem1 vs control, on feature ftr2
+Scale 20	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+
+Test: elem2 vs control, on feature ftr1
+Scale 50	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+
+Test: elem2 vs control, on feature ftr2
+Scale 20	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.561	0.653	0.733	0.829	0.899	0.918	0.918	0.918	0.918	0.926	0.926	0.926	0.926	0.965	0.926	0.922	0.922	0.922	0.98	0.922	0.922	0.922	0.922	0.922	0.922	0.922	0.929	0.922	0.922	0.922	0.922	0.922	0.922
+
+Test: elem3 vs control, on feature ftr1
+Scale 50	0.756	0.756	0.644	0.644	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.117	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.186	0.698	0.885	0.732	0.602	0.474	0.381	0.381	0.455	0.607	0.822	0.822	0.689
+
+Test: elem3 vs control, on feature ftr2
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+
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Binary file iwtomics-1.0/test-data/output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf has changed
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Binary file iwtomics-1.0/test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt has changed
Binary file iwtomics-1.0/test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf has changed
Binary file iwtomics-1.0/test-data/output_testandplot/._iwtomics.testandplot.tests.txt has changed
Binary file iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.RData has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,312 @@
+Test: elem1 vs control, on feature ftr1
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+
+Test: elem1 vs control, on feature ftr2
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+Scale 44	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 43	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 42	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 41	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 40	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 39	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 38	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 37	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 36	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 35	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 34	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 33	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 32	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 31	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 30	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 29	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 28	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 27	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 26	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 25	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 24	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 23	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 22	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 21	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 20	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 19	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 18	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
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+Scale 8	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 7	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 6	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 5	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 4	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 3	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 2	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 1	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+
+Test: elem2 vs control, on feature ftr1
+Scale 50	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 49	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 48	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 47	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 46	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 45	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 44	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 43	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 42	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 41	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 40	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 39	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 38	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 37	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 36	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 35	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 34	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 33	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 32	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 31	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 30	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 29	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 28	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 27	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 26	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 25	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 24	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 23	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 22	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 21	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 20	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 19	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 18	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 17	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 16	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 15	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 14	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 13	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 12	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 11	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 10	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 9	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 8	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 7	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 6	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 5	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 4	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 3	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 2	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 1	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+
+Test: elem2 vs control, on feature ftr2
+Scale 50	0.989	0.937	0.845	0.825	0.825	0.825	0.825	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 49	0.989	0.937	0.845	0.797	0.797	0.797	0.797	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 48	0.989	0.937	0.845	0.772	0.772	0.772	0.795	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 47	0.989	0.937	0.845	0.759	0.755	0.761	0.795	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 46	0.989	0.937	0.845	0.759	0.755	0.761	0.795	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 45	0.989	0.937	0.845	0.759	0.712	0.761	0.795	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 44	0.989	0.937	0.845	0.759	0.696	0.715	0.795	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 43	0.989	0.937	0.845	0.759	0.683	0.683	0.744	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 42	0.989	0.937	0.845	0.759	0.68	0.68	0.712	0.787	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 41	0.989	0.937	0.845	0.759	0.68	0.68	0.686	0.759	0.821	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 40	0.989	0.937	0.845	0.759	0.673	0.673	0.673	0.734	0.79	0.834	0.852	0.852	0.852	0.852	0.852	0.852	0.852	0.852	0.852	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 39	0.989	0.937	0.845	0.759	0.65	0.65	0.652	0.718	0.767	0.804	0.827	0.841	0.841	0.841	0.841	0.841	0.841	0.841	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 38	0.989	0.937	0.845	0.759	0.644	0.626	0.639	0.7	0.758	0.802	0.805	0.805	0.834	0.834	0.834	0.834	0.834	0.834	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 37	0.989	0.937	0.845	0.759	0.644	0.605	0.625	0.681	0.739	0.802	0.805	0.801	0.801	0.825	0.825	0.825	0.825	0.825	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 36	0.989	0.937	0.845	0.759	0.644	0.593	0.613	0.678	0.739	0.802	0.805	0.801	0.801	0.819	0.808	0.808	0.808	0.821	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
+Scale 35	0.989	0.937	0.845	0.759	0.644	0.582	0.613	0.678	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.789	0.794	0.821	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
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+
+Test: elem3 vs control, on feature ftr1
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+Scale 10	0.756	0.756	0.638	0.638	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.076	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.122	0.698	0.885	0.732	0.602	0.474	0.36	0.348	0.455	0.607	0.822	0.822	0.689
+Scale 9	0.756	0.756	0.595	0.595	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.076	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.122	0.698	0.885	0.732	0.602	0.474	0.36	0.348	0.455	0.607	0.822	0.822	0.689
+Scale 8	0.756	0.756	0.552	0.551	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.076	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.122	0.698	0.885	0.732	0.602	0.474	0.36	0.348	0.455	0.607	0.822	0.822	0.689
+Scale 7	0.756	0.756	0.552	0.548	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.056	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.122	0.698	0.885	0.732	0.602	0.474	0.36	0.348	0.455	0.607	0.822	0.822	0.689
+Scale 6	0.756	0.756	0.552	0.499	0.662	0.823	0.943	1	0.986	0.927	0.806	0.472	0.035	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.121	0.698	0.885	0.732	0.602	0.474	0.36	0.348	0.455	0.607	0.822	0.822	0.689
+Scale 5	0.756	0.756	0.552	0.431	0.611	0.823	0.943	1	0.986	0.927	0.806	0.404	0.019	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.121	0.698	0.885	0.732	0.602	0.474	0.307	0.298	0.455	0.607	0.822	0.822	0.689
+Scale 4	0.756	0.756	0.552	0.414	0.527	0.795	0.943	1	0.986	0.927	0.758	0.323	0.011	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.094	0.698	0.885	0.732	0.602	0.416	0.24	0.218	0.411	0.607	0.822	0.822	0.689
+Scale 3	0.756	0.756	0.552	0.328	0.439	0.722	0.943	1	0.986	0.902	0.672	0.242	0.006	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.057	0.698	0.885	0.732	0.538	0.325	0.186	0.149	0.294	0.597	0.822	0.822	0.689
+Scale 2	0.756	0.756	0.461	0.237	0.32	0.607	0.906	1	0.986	0.826	0.543	0.164	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.034	0.688	0.885	0.732	0.424	0.263	0.151	0.11	0.205	0.478	0.822	0.822	0.598
+Scale 1	0.753	0.699	0.315	0.187	0.228	0.455	0.803	1	0.935	0.698	0.387	0.071	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.007	0.546	0.885	0.578	0.334	0.195	0.122	0.096	0.13	0.319	0.767	0.783	0.496
+
+Test: elem3 vs control, on feature ftr2
+Scale 50	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 49	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 48	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 47	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 46	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 45	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 44	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 43	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 42	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 41	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 40	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 39	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 38	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 37	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 36	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 35	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 34	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 33	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 32	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 31	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 30	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 29	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 28	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 27	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 26	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 25	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 24	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 23	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.229	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 22	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.8	0.21	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 21	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.906	0.906	0.9	0.792	0.193	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 20	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.9	0.9	0.9	0.792	0.181	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 19	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.9	0.9	0.9	0.792	0.165	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 18	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.9	0.9	0.9	0.78	0.142	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 17	0.907	0.907	0.907	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.899	0.899	0.89	0.742	0.129	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 16	0.881	0.891	0.892	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.896	0.891	0.865	0.709	0.122	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 15	0.861	0.861	0.892	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.885	0.861	0.849	0.701	0.113	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 14	0.853	0.853	0.859	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.892	0.854	0.844	0.844	0.691	0.105	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 13	0.852	0.852	0.852	0.882	0.923	0.949	0.923	0.923	0.923	0.923	0.941	0.941	0.923	0.923	0.923	0.923	0.923	0.92	0.871	0.841	0.841	0.835	0.654	0.092	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 12	0.837	0.837	0.837	0.863	0.898	0.949	0.915	0.915	0.915	0.915	0.941	0.941	0.915	0.915	0.915	0.915	0.915	0.893	0.853	0.832	0.832	0.819	0.603	0.078	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 11	0.81	0.81	0.82	0.853	0.883	0.949	0.89	0.89	0.89	0.89	0.941	0.941	0.89	0.89	0.89	0.89	0.895	0.878	0.842	0.818	0.813	0.774	0.562	0.07	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 10	0.778	0.778	0.802	0.838	0.883	0.949	0.883	0.883	0.883	0.883	0.941	0.941	0.883	0.88	0.88	0.88	0.895	0.878	0.839	0.798	0.756	0.732	0.528	0.064	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 9	0.743	0.743	0.763	0.827	0.883	0.949	0.883	0.883	0.883	0.883	0.941	0.941	0.883	0.88	0.88	0.88	0.895	0.878	0.805	0.737	0.708	0.708	0.517	0.051	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 8	0.724	0.724	0.724	0.782	0.866	0.949	0.875	0.875	0.875	0.88	0.941	0.941	0.88	0.88	0.88	0.88	0.895	0.858	0.75	0.697	0.697	0.697	0.499	0.038	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 7	0.71	0.71	0.71	0.731	0.826	0.949	0.861	0.861	0.861	0.88	0.941	0.941	0.863	0.863	0.863	0.863	0.895	0.801	0.695	0.685	0.685	0.685	0.436	0.029	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 6	0.681	0.671	0.671	0.695	0.78	0.949	0.823	0.823	0.823	0.88	0.941	0.941	0.859	0.82	0.82	0.824	0.895	0.74	0.667	0.667	0.667	0.632	0.349	0.023	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 5	0.681	0.622	0.63	0.669	0.759	0.949	0.822	0.767	0.813	0.88	0.941	0.941	0.859	0.801	0.756	0.824	0.895	0.74	0.653	0.634	0.608	0.545	0.306	0.015	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 4	0.681	0.622	0.588	0.655	0.759	0.949	0.822	0.734	0.787	0.88	0.941	0.941	0.859	0.773	0.738	0.824	0.895	0.74	0.638	0.569	0.564	0.545	0.278	0.009	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 3	0.681	0.622	0.588	0.599	0.759	0.949	0.822	0.726	0.706	0.88	0.941	0.941	0.859	0.672	0.738	0.824	0.895	0.74	0.567	0.512	0.564	0.545	0.234	0.006	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 2	0.681	0.622	0.5	0.5	0.717	0.949	0.822	0.578	0.586	0.784	0.941	0.941	0.759	0.534	0.611	0.824	0.895	0.662	0.45	0.47	0.564	0.545	0.158	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+Scale 1	0.681	0.553	0.434	0.417	0.582	0.949	0.66	0.476	0.513	0.664	0.889	0.868	0.592	0.461	0.487	0.708	0.895	0.512	0.342	0.402	0.564	0.494	0.074	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
+
Binary file iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.selectedfeatures.txt	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,1 @@
+ftr1	ftr2
Binary file iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.summaryplot.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/test-data/output_testandplot/iwtomics.testandplot.tests.txt	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,1 @@
+elem1 vs control	elem2 vs control	elem3 vs control
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/testandplot.R	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,99 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+  args=commandArgs(TRUE)
+  
+  # get args names and values
+  args_values=strsplit(args,'=')
+  args_names=unlist(lapply(args_values,function(arg) arg[1]))
+  names(args_values)=args_names
+  args_values=lapply(args_values,function(arg) arg[2])
+  # read filenames
+  adjustedpvaluematrix=args_values$adjustedpvaluematrix
+  iwtomicsrespdf=args_values$iwtomicsrespdf
+  iwtomicssumpdf=args_values$iwtomicssumpdf
+  regionids=args_values$regionids
+  featureids=args_values$featureids
+  rdatafile=args_values$rdatafile
+  iwtomicsrdata=args_values$iwtomicsrdata
+  iwtomicstests=args_values$iwtomicstests
+  iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
+  # read parameters (from region1 on)
+  i_region1=which(args_names=='region1')
+  for(i in i_region1:length(args)){
+    eval(parse(text=args[[i]]))
+  }
+  
+  # load RData
+  load(rdatafile)
+  # read regionids and featureids
+  regionids=as.character(read.delim(regionids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  featureids=as.character(read.delim(featureids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  # retrieve region1, region2 and features_subset ids and check they are in the RData
+  id_region1=regionids[region1]
+  id_region2=regionids[region2]
+  id_features_subset=featureids[features_subset]
+  if(length(setdiff(c(id_region1,id_region2),idRegions(regionsFeatures)))!=0){
+    write("Wrong region ids.", stderr())
+    quit(save="no", status=10)
+  }
+  if(length(setdiff(id_features_subset,idFeatures(regionsFeatures)))!=0){
+    write("Wrong feature ids.", stderr())
+    quit(save="no", status=20)
+  }
+  if(sum(duplicated(paste0(id_region1,id_region2)))){
+    write("Same test repeated multiple times.", stderr())
+    quit(save="no", status=30)
+  }
+  
+  # perform test
+  tryCatch({
+    # fix repeated probs
+    if(statistics=='quantile'){
+      # fix repeated probs
+      testprobs=sort(unique(testprobs))
+    }else{
+      testprobs=0.5
+    }
+    regionsFeatures_test=IWTomicsTest(regionsFeatures,id_region1,id_region2,id_features_subset,
+                                      statistics=statistics,probs=testprobs,B=B)
+    # create adjustedvaluematrix output
+    for(test in seq_along(id_region1)){
+      for(id_feature in id_features_subset){
+        write(paste0('Test: ',id_region1[test],' vs ',id_region2[test],', on feature ',id_feature),
+              file=adjustedpvaluematrix,append=TRUE,sep='\t')
+        pval=regionsFeatures_test@test$result[[test]][[id_feature]]$adjusted_pval_matrix
+        row.names(pval)=paste('Scale',rev(seq_len(nrow(pval))))
+        write.table(pval,file=adjustedpvaluematrix,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
+        write('',file=adjustedpvaluematrix,append=TRUE,sep='\t')
+      }
+    }
+  }, error = function(err) {
+    write("Testing error.", stderr())
+    quit(save="no", status=40) #error testing
+  })
+  
+  # plot test results
+  pdf(iwtomicsrespdf,width=5,height=7)
+  if(plottype=='boxplot'){
+    # fix repeated probs
+    probs=sort(unique(probs))
+  }else{
+    probs=c(0.25,0.5,0.75)
+  }
+  plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
+  dev.off()
+  
+  # plot summary results
+  if(groupby!='none'){
+    pdf(iwtomicssumpdf,width=15,height=10)
+    plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,ask=FALSE,append=TRUE)
+    dev.off()
+  }
+  
+  # create output
+  write.table(as.data.frame(t(paste(id_region1,'vs',id_region2))),file=iwtomicstests,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  write.table(as.data.frame(t(idFeatures(regionsFeatures_test))),file=iwtomicsselectedfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  save(regionsFeatures_test,file=iwtomicsrdata)
+}else{
+  write("Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
+  quit(save="no", status=255)
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iwtomics-1.0/testandplot.xml	Fri Oct 06 11:03:56 2017 -0400
@@ -0,0 +1,201 @@
+<tool id="iwtomics_testandplot" name="IWTomics Test" version="@VERSION@.0">
+  <description>and Plot</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+
+  <command detect_errors="exit_code">
+<![CDATA[
+    Rscript '$__tool_directory__/testandplot.R' adjustedpvaluematrix='${adjustedpvaluematrix}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' iwtomicsrdata='${iwtomicsrdata}' iwtomicstests='${iwtomicstests}' iwtomicsselectedfeatures='${iwtomicsselectedfeatures}'
+      regionids='${regionids}'
+      featureids='${featureids}'
+      rdatafile='${rdata}'
+
+      #set region1 = ','.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
+      #set region2 = ','.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
+      region1='c(${region1})'
+      region2='c(${region2})'
+
+      features_subset='c(${featureslist})'
+
+      statistics="'${conditionalstatistics.statistics}'"
+      #if $conditionalstatistics.statistics == "quantile":
+        #set probabilities = ','.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
+        testprobs='c(${probabilities})'
+      #end if
+
+      B='${permutations}'
+
+      testalpha='${plotres.alpha}'
+      average='${plotres.average}'
+      size='${plotres.size}'
+      plottype="'${plotres.conditionalplottype.plottype}'"
+      #if $plotres.conditionalplottype.plottype == "boxplot":
+        #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #if $probs != "":
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
+        #else:
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
+        #end if
+      #end if
+
+      groupby="'${plotsum.conditionalgroupby.groupby}'"
+      #if $plotsum.conditionalgroupby.groupby == "test":
+        summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
+        only_significant='${plotsum.conditionalgroupby.testonlysig}'
+      #elif $plotsum.conditionalgroupby.groupby == "feature":
+        summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
+        only_significant='${plotsum.conditionalgroupby.featureonlysig}'
+      #end if
+]]>
+  </command>
+
+  <inputs>
+    <!-- RData -->
+    <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object" help="File created by 'IWTomics Load Smooth and Plot'." />
+    <!-- region IDs -->
+    <param format="tabular" name="regionids" type="data" label="Select region dataset IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
+    <!-- feature IDs -->
+    <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
+
+    <!-- repeat region ids -->
+    <section name="regionssection" title="Select regions for Interval-Wise Testing" expanded="True" help="IDs of the region datasets to be tested.">
+      <repeat name="regions" title="Two-sample test" min="1">
+        <param name="region0" type="data_column" data_ref="regionids" numerical="False" label="Region 1" multiple="False" use_header_names="True" />
+        <param name="region1" type="data_column" data_ref="regionids" numerical="False" label="Region 2" multiple="False" use_header_names="True" />
+      </repeat>
+    </section>
+
+    <!-- feature ids list -->
+    <param name="featureslist" type="data_column" data_ref="featureids" numerical="False" label="Select features" multiple="True" use_header_names="True" help="IDs of the features to be tested." />
+
+    <!-- conditional statistics -->
+    <conditional name="conditionalstatistics">
+      <!-- statistics -->
+      <param name="statistics" type="select" label="Test statistics">
+        <option value="mean">Mean difference</option>
+        <option value="median">Median difference</option>
+        <option value="variance">Variance ratio</option>
+        <option value="quantile">Quantile difference(s)</option>
+      </param>
+      <!-- conditional choice: statistics=quantile -->
+      <when value="quantile">
+        <section name="quantilesection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantiles in test statistics.">
+          <repeat name="qprobabilities" title="Probabilities" min="1">
+            <param name="qprob" size="4" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+          </repeat>
+        </section>
+      </when>
+    </conditional>
+
+    <!-- permutations -->
+    <param name="permutations" type="integer" value="1000" min="1" label="Number of permutations" />
+
+    <!-- plot IWTomics results -->
+    <section name="plotres" title="Plot IWTomics test results" expanded="True">
+      <!-- alpha -->
+      <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+      <expand macro="plot-params" />
+    </section>
+
+    <!-- summary plot -->
+    <expand macro="plot-sum" />
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" />
+    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
+    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
+    <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" />
+    <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" />
+    <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="rdata" value="output_loadandplot/iwtomics.loadandplot.RData" ftype="rdata" />
+      <param name="regionids" value="output_loadandplot/iwtomics.loadandplot.regions.txt" ftype="tabular" />
+      <param name="featureids" value="output_loadandplot/iwtomics.loadandplot.features.txt" ftype="tabular" />
+      <repeat name="regions">
+          <param name="region0" value="2" />
+          <param name="region1" value="1" />
+      </repeat>
+      <repeat name="regions">
+          <param name="region0" value="3" />
+          <param name="region1" value="1" />
+      </repeat>
+      <repeat name="regions">
+          <param name="region0" value="4" />
+          <param name="region1" value="1" />
+      </repeat>
+      <param name="featureslist" value="1,2" />
+      <param name="statistics" value="mean" />
+      <param name="permutations" value="1000" />
+      <param name="alpha" value="0.05" />
+      <param name="average" value="TRUE" />
+      <param name="size" value="TRUE" />
+      <param name="plottype" value="boxplot" />
+      <param name="prob0" value="0.25" />
+      <param name="prob1" value="0.5" />
+      <param name="prob2" value="0.75" />
+      <param name="groupby" value="feature" />
+      <param name="featurealphaplot" value="0.05" />
+      <param name="featureonlysig" value="TRUE" />
+      <output name="adjustedpvaluematrix" file="output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt" compare="sim_size" />
+      <output name="iwtomicsrespdf" file="output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf" compare="sim_size" />
+      <output name="iwtomicssumpdf" file="output_testandplot/iwtomics.testandplot.summaryplot.pdf" compare="sim_size" />
+      <output name="iwtomicsrdata" file="output_testandplot/iwtomics.testandplot.RData" compare="sim_size" />
+      <output name="iwtomicstests" file="output_testandplot/iwtomics.testandplot.tests.txt" />
+      <output name="iwtomicsselectedfeatures" file="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" />
+    </test>
+  </tests>
+
+  <help><![CDATA[
+This tool statistically evaluates differences in genomic features between groups of regions along the genome.
+In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise
+Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation
+tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test
+and all possible scales. Moreover, it creates a graphical representation of the Interval-Wise Testing results
+and a summary plot (optional) with p-values at the maximum scale. The tool *IWTomics Plot with Threshold on Test Scale*
+permits to select the scale to be used in the plots.
+
+-----
+
+**Input files**
+
+RData file with the IWTomicsData object, tabular files with region dataset IDs and feature IDs.
+These files are created by the tool *IWTomics Load Smooth and Plot*.
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. TXT file with an adjusted p-value matrix for every test performed. Each matrix contains a p-value curve (row) for every scale considered in the test;
+2. PDF file with the plotted test results;
+3. PDF file with the summary plot;
+4. RData with the IWTomicsData object with the test results;
+5. Test identifiers;
+6. Feature identifiers.
+
+4-6 can be used as input of the tool *IWTomics Plot with Threshold on Test Scale*
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+  ]]></help>
+
+  <expand macro="citations" />
+
+</tool>
--- a/loadandplot.R	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,144 +0,0 @@
-if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
-  args=commandArgs(TRUE)
-  
-  # get args names and values
-  args_values=strsplit(args,'=')
-  args_names=unlist(lapply(args_values,function(arg) arg[1]))
-  names(args_values)=args_names
-  args_values=lapply(args_values,function(arg) arg[2])
-  # read filenames
-  outrdata=args_values$outrdata
-  outregions=args_values$outregions
-  outfeatures=args_values$outfeatures
-  outpdf=args_values$outpdf
-  regionspaths=unlist(strsplit(args_values$regionspaths,'\\|'))
-  if("regionsheaderfile" %in% args_names){
-    # the file regionsheaderfile must contain as first column the (unique) regionsfilenames, 
-    # as second column the corresponding ids and as third column the names
-    tryCatch({
-      regionsheader=read.delim(args_values$regionsheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
-      regionsfilenames=unlist(strsplit(args_values$regionsfilenames,'\\|'))
-      if(length(setdiff(regionsfilenames,row.names(regionsheader)))) {
-        write("IWTomics message: Not all region files are present in the first column of header file for regions.", stderr())
-        quit(save="no", status=11)
-      }
-      id_regions=regionsheader[regionsfilenames,1]
-      name_regions=regionsheader[regionsfilenames,2]
-    }, error = function(err) {
-      write("IWTomics message: An error has occurred reading the header file for regions. Please try again.", stderr())
-      quit(save="no", status=10) #error on header file
-    })
-  }else{
-    eval(parse(text=args[[which(args_names=='regionsgalaxyids')]]))
-    id_regions=paste0('data_',regionsgalaxyids)
-    name_regions=paste0('data_',regionsgalaxyids)
-  }
-  featurespaths=unlist(strsplit(args_values$featurespaths,'\\|'))
-  if("featuresheaderfile" %in% args_names){
-    # the file featuresheaderfile must contain as first column the (unique) featuresfilenames, 
-    # as second column the corresponding ids and as third column the names
-    tryCatch({
-      featuresheader=read.delim(args_values$featuresheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
-      featuresfilenames=unlist(strsplit(args_values$featuresfilenames,'\\|'))
-      if(length(setdiff(featuresfilenames,row.names(featuresheader)))) {
-        write("IWTomics message: Not all feature files are present in the first column of header file for features.", stderr())
-        quit(save="no", status=21)
-      }
-      id_features=featuresheader[featuresfilenames,1]
-      name_features=featuresheader[featuresfilenames,2]
-    }, error = function(err) {
-      write("IWTomics message: An error has occurred reading the header file for features. Please try again.", stderr())
-      quit(save="no", status=20) #error on header file
-    })
-  }else{
-    eval(parse(text=args[[which(args_names=='featuresgalaxyids')]]))
-    id_features=paste0('data_',featuresgalaxyids)
-    name_features=paste0('data_',featuresgalaxyids)
-  }
-  # read parameters (from smoothing on)
-  i_smoothing=which(args_names=='smoothing')
-  for(i in i_smoothing:length(args)){
-    eval(parse(text=args[[i]]))
-  }
-  
-  # load data
-  tryCatch({
-    regionsFeatures=IWTomicsData(regionspaths,featurespaths,alignment,
-                                id_regions,name_regions,id_features,name_features,start.are.0based=start.are.0based)
-  }, error = function(err) {
-    if(grepl('invalid format',err$message)){
-      write("IWTomics message: Not enough columns in input file.", stderr())
-      quit(save="no", status=31) # error, not enough columns in input file
-    }else if(grepl('duplicated regions',err$message)){
-      write("IWTomics message: Duplicated regions in region file.", stderr())
-      quit(save="no", status=32) # error, duplicated regions in region file
-    }else if(grepl('duplicated windows',err$message)){
-      write("IWTomics message: Duplicated windows in feature file.", stderr())
-      quit(save="no", status=33) # error, duplicated windows in feature file
-    }else if(grepl('overlapping windows',err$message)){
-      write("IWTomics message: Overlapping windows in feature file.", stderr())
-      quit(save="no", status=34) # error, overlapping windows in feature file
-    }else if(grepl('not all regions in datasets',err$message)){
-      write("IWTomics message: Windows in feature files do not cover all regions in region files.", stderr())
-      quit(save="no", status=35) # error, windows in feature files do not cover all regions in region files
-    }else if(grepl('ifferent size windows',err$message)){
-      write("IWTomics message: All windows in a feature file must have the same size.", stderr())
-      quit(save="no", status=36) # error, all windows in a feature files must have the same size
-    }
-    #error loading data
-    write("IWTomics message: An error has occurred reading the data. Please try again.", stderr())
-    quit(save="no", status=30)    
- })
-  
-  # smooth data
-  if(smoothing!='no'){
-    tryCatch({
-      if(smoothing=='locpoly'){
-        dist_knots=10
-      }else if(smoothing=='kernel'){
-        degree=3
-        dist_knots=10
-      }else if(smoothing=='splines'){
-        bandwidth=5
-      }
-      if(alignment=='scale'){
-        if(scale==0){
-          regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
-                                bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
-        }else{
-          regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
-                                bandwidth=bandwidth,degree=degree,dist_knots=dist_knots,scale_grid=scale)
-        }
-      }else{
-        regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
-                              bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
-      }
-    }, error = function(err) {
-      write("IWTomics message: An error has occurred smoothing the data. Please try again.", stderr())
-      quit(save="no", status=40) #error on smoothing
-    })
-  }
-  
-  # plot data
-  pdf(outpdf,width=10,height=8)
-  if(plottype=='boxplot'){
-    # fix repeated probs
-    probs=sort(unique(probs))
-  }else{
-    probs=c(0.25,0.5,0.75)
-  }
-  plot(regionsFeatures,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
-  dev.off()
-  
-  # create output
-  #write.table(cbind(unlist(strsplit(args_values$regionsfilenames,'\\|')),idRegions(regionsFeatures),nameRegions(regionsFeatures)),
-              #file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
-  write.table(as.data.frame(t(idRegions(regionsFeatures))),file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
-  #write.table(cbind(unlist(strsplit(args_values$featuresfilenames,'\\|')),idFeatures(regionsFeatures),nameFeatures(regionsFeatures)),
-              #file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
-  write.table(as.data.frame(t(idFeatures(regionsFeatures))),file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
-  save(regionsFeatures,file=outrdata)
-}else{
-  write("IWTomics message: Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
-  quit(save="no", status=255)
-}
\ No newline at end of file
--- a/loadandplot.xml	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,237 +0,0 @@
-<tool id="iwtomics_loadandplot" name="IWTomics Load" version="@VERSION@.0">
-  <description>Smooth and Plot</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements" />
-
-  <command detect_errors="exit_code">
-<![CDATA[
-    Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
-
-      #set region_paths = '|'.join( [ str( $r ) for $r in $regions ] )
-      regionspaths='${region_paths}'
-      #set region_galaxyids = ','.join( [ str( $r.hid ) for $r in $regions ] )
-      regionsgalaxyids='c(${region_galaxyids})'
-      #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] )
-      regionsfilenames='${region_names}'
-      #set region_header = $regionsheader
-      #if $region_header != "":
-        regionsheaderfile='${region_header}'
-      #end if
-      
-      #set feature_paths = '|'.join( [ str( $f ) for $f in $features ] )
-      featurespaths='${feature_paths}'
-      #set feature_galaxyids = ','.join( [ str( $f.hid ) for $f in $features ] )
-      featuresgalaxyids='c(${feature_galaxyids})'
-      #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] )
-      featuresfilenames='${feature_names}'
-      #set feature_header = $featuresheader
-      #if $feature_header != "":
-        featuresheaderfile='${feature_header}'
-      #end if
-
-      smoothing="'${conditionaltype.smoothing}'"
-      start.are.0based='${zerobased}'
-      #if $conditionaltype.smoothing == 'no':
-        alignment="'${conditionaltype.alignment}'"
-      #elif $conditionaltype.smoothing == 'locpoly':
-        bandwidth='${conditionaltype.locpolybandwidth}'
-        degree='${conditionaltype.locpolydegree}'
-        alignment="'${conditionaltype.conditionalscale.alignment}'"
-      #elif $conditionaltype.smoothing == 'kernel':
-        bandwidth='${conditionaltype.kernelbandwidth}'
-        alignment="'${conditionaltype.conditionalscale.alignment}'"
-      #elif $conditionaltype.smoothing == 'splines':
-        degree='${conditionaltype.splinesdegree}'
-        dist_knots='${conditionaltype.splinesdistknots}'
-        alignment="'${conditionaltype.conditionalscale.alignment}'"
-      #end if
-
-      #if $conditionaltype.smoothing != 'no':
-        #if $conditionaltype.conditionalscale.alignment == 'scale':
-          scale='${conditionaltype.conditionalscale.scalegrid}'
-          fill_gaps='TRUE'
-        #else
-          fill_gaps='${conditionaltype.conditionalscale.fillgaps}'
-        #end if
-      #end if
-
-      average='${plotres.average}'
-      size='${plotres.size}'
-      plottype="'${plotres.conditionalplottype.plottype}'"
-      #if $plotres.conditionalplottype.plottype == 'boxplot':
-        #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
-        #if $probs != "":
-          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
-        #else:
-          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
-        #end if
-      #end if      
-]]>
-  </command>
-
-  <inputs>
-    <!-- regions -->
-    <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
-    <param format="tabular" name="regionsheader" type="data" label="Insert header file for regions (optional)" optional="true" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output." />
-
-    <!-- features -->
-    <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" />
-    <param format="tabular" name="featuresheader" type="data" label="Insert header file for features (optional)" optional="true" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output." />
-
-    <!-- zero-base one-base -->
-    <param name="zerobased" type="select" label="Start positions are:" multiple="false" help="">
-      <option value="TRUE">0-based</option>
-      <option value="FALSE">1-based</option>
-    </param>
-
-    <!-- conditional smoothing -->
-    <conditional name="conditionaltype">
-      <!-- smoothing -->
-      <param name="smoothing" type="select" label="Smoothing" help="Type of smoothing to be applied to the feature curves.">
-        <option value="no">No</option>
-        <option value="locpoly">Local Polynomials</option>
-        <option value="kernel">Gaussian Kernel</option>
-        <option value="splines">B-Splines</option>
-      </param>
-      <!-- conditional choice: smoothing=no -->
-      <when value="no">
-        <expand macro="alignment" />
-      </when>
-      <!-- conditional choice: smoothing=locpoly -->
-      <when value="locpoly">
-        <param name="locpolybandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
-        <param name="locpolydegree" type="integer" value="3" min="0" label="Degree of local polynomial" help="" />
-        <!-- conditional region alignment -->
-        <expand macro="alignment-s" />
-      </when>
-      <!-- conditional choice: smoothing=kernel -->
-      <when value="kernel">
-        <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
-        <!-- conditional region alignment -->
-        <expand macro="alignment-s" />
-      </when>
-      <!-- conditional choice: smoothing=splines -->
-      <when value="splines">
-        <param name="splinesdegree" type="integer" value="3" min="0" label="Degree of B-splines" help="" />
-        <param name="splinesdistknots" type="integer" value="10" min="2" label="Distance between nodes (approximate)" help="" />
-        <!-- conditional region alignment -->
-        <expand macro="alignment-s" />
-      </when>
-    </conditional>
-
-    <!-- plot IWTomics results -->
-    <section name="plotres" title="Plot data" expanded="True">
-      <expand macro="plot-params" />
-    </section>
-  </inputs>
-
-  <outputs>
-    <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" />
-    <data format="tabular" name="outregions" label="${tool.name} on ${on_string}: Region Dataset IDs" from_work_dir="iwtomics.loadandplot.regions.txt" />
-    <data format="tabular" name="outfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.loadandplot.features.txt" />
-    <data format="pdf" name="outpdf" label="${tool.name} on ${on_string}: Plotted Data" from_work_dir="iwtomics.loadandplot.pdf" />
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="regions" value="input/Controls_regions.bed,input/Elements1_regions.bed,input/Elements2_regions.bed,input/Elements3_regions.bed" ftype="bed" />
-      <param name="regionsheader" value="input/regions.header.txt" ftype="tabular" />
-      <param name="features" value="input/Feature1.bed,input/Feature2.bed" ftype="bed" />
-      <param name="featuresheader" value="input/features.header.bed.txt" ftype="tabular" />
-      <param name="zerobased" value="TRUE" />
-      <param name="smoothing" value="kernel" />
-      <param name="alignment" value="center" />
-      <param name="kernelbandwidth" value="5" />
-      <param name="fillgaps" value="TRUE" />
-      <param name="average" value="TRUE" />
-      <param name="size" value="TRUE" />
-      <param name="plottype" value="boxplot" />
-      <param name="prob0" value="0.25" />
-      <param name="prob1" value="0.5" />
-      <param name="prob2" value="0.75" />
-      <output name="outrdata" file="output_loadandplot/iwtomics.loadandplot.RData" compare="sim_size" />
-      <output name="outregions" file="output_loadandplot/iwtomics.loadandplot.regions.txt" />
-      <output name="outfeatures" file="output_loadandplot/iwtomics.loadandplot.features.txt" />
-      <output name="outpdf" file="output_loadandplot/iwtomics.loadandplot.pdf" compare="sim_size" />
-    </test>
-  </tests>
-
-  <help><![CDATA[
-This tool imports a collection of genomic region datasets, and associates to each region
-multiple genomic feature measurements. It allows to align the regions in multiple ways
-(center, left, right or scale alignment), to smooth the feature curves (possibly filling gaps in the
-measurements) and to create a graphical representation of the feature measurements in each
-region datasets (aligned curves or pointwise quantile curves).
-
------
-
-**Region datasets**
-
-Each region dataset can be provided as a BED or Tabular file with tab delimited columns chr
-start end (extra columns present in the input file are ignored). Regions can be of different
-length::
-
-    chr2  49960150  50060150
-    chr2  55912445  56012445
-    ...
-
------
-
-**Feature measurements**
-
-Feature measurements corresponding to all the regions can be provided as a BED or Tabular
-file with tab delimited columns chr start end value::
-
-    chr2  49960150  49962150  0.9426
-    chr2  49962150  49964150  0.7816
-    ...
-
-Each feature must be measured in windows of a fixed size inside all the regions (missing
-values must be indicated as NA). Another way to import feature measurements is from a
-Tabular file with the first three columns chr start end corresponding to the different genomic
-regions, followed on the same row by all the measurements in fixed-size windows::
-
-    chr2  49960150  50060150  0.9426  0.7816  0.8921  ...  ...  1.2063
-    chr2  55912445  56012445  0.8719  0.9975  1.1619  ...  ...  0.9601
-    ...
-
------
-
-**Output**
-
-The tool returns:
-
-1. RData with the IWTomicsData object, that stores the aligned genomic region datasets, and their associated feature measurements;
-2. Region dataset identifiers;
-3. Feature identifiers;
-4. PDF file with the plotted data.
-
-1-3 can be used as input of the tool *IWTomics Test and Plot*
-
------
-
-.. class:: infomark
-
-**Notes**
-
-This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy - fabio.cumbo@iasi.cnr.it) and Marzia A. Cremona (The Pennsylvania State University, USA - mac78@psu.edu).
-
-It implements a simplified version of the methods *smooth* and *plot* for *IWTomicsData* objects.
-The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
-
-.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
-
-Example data can be found at:
-
-1. Simulated_data_
-2. ETn_data_
-
-.. _Simulated_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-example
-.. _ETn_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-etn-example
-  ]]></help>
-
-  <expand macro="citations" />
-
-</tool>
--- a/macros.xml	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,106 +0,0 @@
-<macros>
-    <token name="@VERSION@">1.0.0</token>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="3.3.1">r-base</requirement>
-            <requirement type="package" version="@VERSION@">bioconductor-iwtomics</requirement>
-        </requirements>
-    </xml>
-    
-    <xml name="alignment-s">
-        <conditional name="conditionalscale">
-            <param name="alignment" type="select" label="Region alignment" help="">
-                <option value="center">Center - Alignment on the central position</option>
-                <option value="left">Left - Alignment on the starting position</option>
-                <option value="right">Right - Alignment on the ending position</option>
-                <option value="scale">Scale - Scaling all regions to the same length</option>
-            </param>
-            <when value="center">
-                <!-- fill gaps -->
-                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
-            </when>
-            <when value="left">
-                <!-- fill gaps -->
-                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
-            </when>
-            <when value="right">
-                <!-- fill gaps -->
-                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
-            </when>
-            <when value="scale">
-                <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
-            </when>
-        </conditional>
-    </xml>
-
-    <xml name="alignment">
-        <param name="alignment" type="select" label="Region alignment" help="">
-            <option value="center">Center - Alignment on the central position</option>
-            <option value="left">Left - Alignment on the starting position</option>
-            <option value="right">Right - Alignment on the ending position</option>
-        </param>
-    </xml>
-
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1080/10485252.2017.1306627</citation>
-            <citation type="bibtex">
-                @MANUAL{
-                        iwtomics,
-                        author = {Cremona, M.A. and Pini, A. and Chiaromonte, F. and Vantini, S.},
-                        title = {IWTomics: Interval-Wise Testing for Omics Data},
-                        note = {R package version 1.0.0},
-                        year = {2017}
-                }
-            </citation>
-        </citations>
-    </xml>
-
-    <xml name="plot-params">
-        <!-- average -->
-        <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
-        <!-- average -->
-        <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
-        <!-- conditional plot type -->
-        <conditional name="conditionalplottype">
-            <!-- plot type -->
-            <param name="plottype" type="select" label="Plot type">
-            <option value="boxplot">Pointwise quantile curves (boxplot)</option>
-            <option value="curves">Curves (aligned)</option>
-            </param>
-            <!-- conditional choice: plottype=boxplot -->
-            <when value="boxplot">
-            <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
-                <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
-                <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
-                <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
-                <repeat name="probabilities" title="Probabilities">
-                <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
-                </repeat>
-            </section>
-            </when>
-        </conditional>
-    </xml>
-
-    <xml name="plot-sum">
-        <section name="plotsum" title="Summary plot" expanded="True">
-            <!-- conditional group by -->
-            <conditional name="conditionalgroupby">
-                <!-- group by -->
-                <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
-                <option value="none">No plot</option>
-                <option value="test">Group by test</option>
-                <option value="feature">Group by feature</option>
-                </param>
-                <when value="test">
-                <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
-                <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
-                </when>
-                <when value="feature">
-                <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
-                <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
-                </when>
-            </conditional>
-        </section>
-    </xml>
-</macros>
\ No newline at end of file
--- a/plotwithscale.R	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
-  args=commandArgs(TRUE)
-  
-  # get args names and values
-  args_values=strsplit(args,'=')
-  args_names=unlist(lapply(args_values,function(arg) arg[1]))
-  names(args_values)=args_names
-  args_values=lapply(args_values,function(arg) arg[2])
-  # read filenames
-  adjustedpvalue=args_values$adjustedpvalue
-  iwtomicsrespdf=args_values$iwtomicsrespdf
-  iwtomicssumpdf=args_values$iwtomicssumpdf
-  iwtomicsrdata=args_values$iwtomicsrdata
-  iwtomicstests=args_values$iwtomicstests
-  iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
-  test_subset=paste0('c(',strsplit(args_values$test_subset,'\\|')[[1]],')')
-  feature_subset=paste0('c(',strsplit(args_values$feature_subset,'\\|')[[1]],')')
-  # read parameters (from test_subset on)
-  i_scale_subset=which(args_names=='scale_subset')
-  for(i in i_scale_subset:length(args)){
-    eval(parse(text=args[[i]]))
-  }
-  
-  # load RData
-  load(iwtomicsrdata)
-  # read testids and featureids and check them
-  unlisted=lapply(seq_along(test_subset),
-                   function(i){
-                     test_subset_i=eval(parse(text=test_subset[i]))
-                     feature_subset_i=eval(parse(text=feature_subset[i]))
-                     test_subset_i=rep(test_subset_i,each=length(feature_subset_i))
-                     feature_subset_i=rep(feature_subset_i,length.out=length(test_subset_i))
-                     scale_subset_i=rep(scale_subset[i],length(test_subset_i))
-                     return(list(test_subset=test_subset_i,feature_subset=feature_subset_i,scale_subset=scale_subset_i))
-                   })
-  test_subset=unlist(lapply(unlisted,function(l) l$test_subset))
-  feature_subset=unlist(lapply(unlisted,function(l) l$feature_subset))
-  scale_subset=unlist(lapply(unlisted,function(l) l$scale_subset))
-  testids=as.character(read.delim(iwtomicstests,header=FALSE,sep='\t',stringsAsFactors=FALSE))
-  featureids=as.character(read.delim(iwtomicsselectedfeatures,header=FALSE,sep='\t',stringsAsFactors=FALSE))
-  id_features_subset=featureids[feature_subset]
-  if(sum(testids!=paste(testInput(regionsFeatures_test)$id_region1,'vs',testInput(regionsFeatures_test)$id_region2))){
-    write("Wrong test ids.", stderr())
-    quit(save="no", status=10)
-  }
-  if(sum(featureids!=idFeatures(regionsFeatures_test))){
-    write("Wrong feature ids.", stderr())
-    quit(save="no", status=20)
-  }
-  # retrieve test and features_subset ids
-  id_features_subset=featureids[feature_subset]
-  if(sum(duplicated(paste0(test_subset,id_features_subset)))){
-    write("Two scale thresholds selected for the same test and feature.", stderr())
-    quit(save="no", status=30)
-  }
-  # If scale_subset=0, do not change the threshold
-  default=(scale_subset==0)
-  scale_subset=scale_subset[!default]
-  test_subset=test_subset[!default]
-  id_features_subset=id_features_subset[!default]
-  
-  # get scale threshold
-  scale_threshold=lapply(regionsFeatures_test@test$result,
-                         function(result) unlist(lapply(result,function(feature) feature$max_scale)))
-  for(i in seq_along(test_subset)){
-    if(scale_threshold[[test_subset[i]]][id_features_subset[i]]<scale_subset[i]){
-      write("Scale threshold too high.", stderr())
-      quit(save="no", status=40)
-    }
-    scale_threshold[[test_subset[i]]][id_features_subset[i]]=scale_subset[i]
-  }
-  
-  # create adjustedvalue output
-  pval=adjusted_pval(regionsFeatures_test,scale_threshold=scale_threshold)
-  for(test in seq_along(pval)){
-    for(id_feature in idFeatures(regionsFeatures_test)){
-      write(paste0('Test: ',testids[test],', on feature ',id_feature),
-              file=adjustedpvalue,append=TRUE,sep='\t')
-        pval_i=as.data.frame(t(pval[[test]][[id_feature]]))
-        row.names(pval_i)=paste('Scale',scale_threshold[[test]][[id_feature]])
-        write.table(pval_i,file=adjustedpvalue,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
-        write('',file=adjustedpvalue,append=TRUE,sep='\t')
-      }
-    }
-  
-  
-  # plot test results
-  pdf(iwtomicsrespdf,width=5,height=7)
-  if(plottype=='boxplot'){
-    # fix repeated probs
-    probs=sort(unique(probs))
-  }else{
-    probs=c(0.25,0.5,0.75)
-  }
-  plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,scale_threshold=scale_threshold,ask=FALSE)
-  dev.off()
-  
-  # plot summary results
-  if(groupby!='none'){
-    tryCatch({
-      pdf(iwtomicssumpdf,width=15,height=10)
-      plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,scale_threshold=scale_threshold,ask=FALSE,append=TRUE)
-      dev.off()
-    }, error = function(err) {
-      if (grepl('selected features with different resolution',err$message)) {
-        write("Group by 'test' but selected features with different resolution.", stderr())
-        quit(save="no", status=50) #error: groupby 'test' but selected features with different resolution.
-      }
-      write("Summary plot error. Please try again.", stderr())
-      quit(save="no", status=60) #error 
-    })
-  }
-  
-}else{
-  write("Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
-  quit(save="no", status=255)
-}
\ No newline at end of file
--- a/plotwithscale.xml	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,149 +0,0 @@
-<tool id="iwtomics_plotwithscale" name="IWTomics Plot with Threshold" version="@VERSION@.0">
-  <description>on Test Scale</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements" />
-  
-  <command detect_errors="exit_code">
-<![CDATA[
-    Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
-      iwtomicsrdata='${rdata}'
-      iwtomicstests='${testids}'
-      iwtomicsselectedfeatures='${featureids}'
-
-      #set test_subset = '|'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
-      test_subset='${test_subset}'
-      #set feature_subset = '|'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
-      feature_subset='${feature_subset}'
-      #set scale_subset = ','.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
-      scale_subset='c(${scale_subset})'
-
-      testalpha='${plotres.alpha}'
-      average='${plotres.average}'
-      size='${plotres.size}'
-      plottype="'${plotres.conditionalplottype.plottype}'"
-      #if $plotres.conditionalplottype.plottype == 'boxplot':
-        #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
-        #if $probs != "":
-          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
-        #else:
-          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
-        #end if
-      #end if
-
-      groupby="'${plotsum.conditionalgroupby.groupby}'"
-      #if $plotsum.conditionalgroupby.groupby == "test":
-        summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
-        only_significant='${plotsum.conditionalgroupby.testonlysig}'
-      #elif $plotsum.conditionalgroupby.groupby == "feature":
-        summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
-        only_significant='${plotsum.conditionalgroupby.featureonlysig}'
-      #end if
-]]>
-  </command>
-
-  <inputs>
-    <!-- RData -->
-    <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object with test results" help="File created by 'IWTomics Test and Plot'." />
-    <!-- test IDs -->
-    <param format="tabular" name="testids" type="data" label="Select test IDs" help="File created by 'IWTomics Test and Plot'." />
-    <!-- feature IDs -->
-    <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Test and Plot'." />
-
-    <!-- repeat threshold on test scale -->
-    <section name="scalesection" title="Select scale for Interval-Wise Testing and plot" expanded="True" help="Maximum interval length for the p-value adjustment. If 0 the maximum possible scale is used.">
-      <repeat name="thresholdontestscale" title="Threshold on test scale" min="1">
-        <param name="test" type="data_column" data_ref="testids" numerical="False" label="Test ID" multiple="True" use_header_names="True" />
-        <param name="feature" type="data_column" data_ref="featureids" numerical="False" label="Feature ID" multiple="True" use_header_names="True" />
-        <param name="scale" type="integer" value="0" min="0" label="Scale" />
-      </repeat>
-    </section>
-
-    <!-- plot IWTomics results -->
-    <section name="plotres" title="Plot IWTomics test results" expanded="True">
-      <!-- alpha -->
-      <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
-      <expand macro="plot-params" />
-    </section>
-
-    <!-- summary plot -->
-    <expand macro="plot-sum" />
-  </inputs>
-
-  <outputs>
-    <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" />
-    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" />
-    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" />
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="rdata" value="output_testandplot/iwtomics.testandplot.RData" ftype="rdata" />
-      <param name="testids" value="output_testandplot/iwtomics.testandplot.tests.txt" ftype="tabular" />
-      <param name="featureids" value="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" ftype="tabular" />
-      <repeat name="thresholdontestscale">
-        <param name="test" value="1" />
-        <param name="feature" value="1" />
-        <param name="scale" value="10" />
-      </repeat>
-      <repeat name="thresholdontestscale">
-        <param name="test" value="1,2,3" />
-        <param name="feature" value="2" />
-        <param name="scale" value="20" />
-      </repeat>
-      <param name="alpha" value="0.05" />
-      <param name="average" value="TRUE" />
-      <param name="size" value="TRUE" />
-      <param name="plottype" value="boxplot" />
-      <param name="prob0" value="0.25" />
-      <param name="prob1" value="0.5" />
-      <param name="prob2" value="0.75" />
-      <param name="groupby" value="feature" />
-      <param name="featurealphaplot" value="0.05" />
-      <param name="featureonlysig" value="TRUE" />
-      <output name="adjustedpvalue" file="output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt" compare="sim_size" />
-      <output name="iwtomicsrespdf" file="output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf" compare="sim_size" />
-      <output name="iwtomicssumpdf" file="output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf" compare="sim_size" />
-    </test>
-  </tests>
-
-  <help><![CDATA[
-This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
-for the different tests performed at the selected scale, and it creates a graphical representation of the
-Interval-Wise Testing results and a summary plot (optional) at the selected scale.
-
------
-
-**Input files**
-
-RData file with the IWTomicsData object with test results, tabular files with test IDs and feature IDs.
-These files are created by the tool *IWTomics Test and Plot*.
-
------
-
-**Output**
-
-The tool returns:
-
-1. TXT file with an adjusted p-value curve for every test performed at the selected scale;
-2. PDF file with the plotted test results;
-3. PDF file with the summary plot.
-
------
-
-.. class:: infomark
-
-**Notes**
-
-This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
-
-It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
-The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
-
-.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
-  ]]></help>
-
-  <expand macro="citations" />
-
-</tool>
--- a/test-data/input/Controls_regions.bed	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-chr1	91399892	91499892
-chr1	116447079	116547079
-chr2	231381109	231481109
-chr3	47386633	47486633
-chr3	99195712	99295712
-chr3	116765114	116865114
-chr3	134345017	134445017
-chr4	68064019	68164019
-chr4	137465811	137565811
-chr4	173293016	173393016
-chr5	59044110	59144110
-chr5	94592763	94692763
-chr5	108436006	108536006
-chr5	110836898	110936898
-chr5	146661073	146761073
-chr6	99727306	99827306
-chr7	88291325	88391325
-chr7	120999784	121099784
-chr8	126860366	126960366
-chr8	127636547	127736547
-chr11	41362564	41462564
-chr11	101741527	101841527
-chr12	15210277	15310277
-chr13	91106037	91206037
-chr13	91518822	91618822
-chr13	98959030	99059030
-chr15	39087176	39187176
-chr17	58542142	58642142
-chr18	12199823	12299823
-chr20	8173704	8273704
-chr21	16255112	16355112
-chr21	45089115	45189115
-chrX	23898983	23998983
-chrX	37029585	37129585
-chrX	103593349	103693349
--- a/test-data/input/Elements1_regions.bed	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-chr2	49960150	50060150
-chr2	55912445	56012445
-chr3	140326750	140426750
-chr4	41772201	41872201
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--- a/test-data/input/Elements2_regions.bed	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
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--- a/test-data/input/Elements3_regions.bed	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
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--- a/test-data/input/Feature1.bed	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5400 +0,0 @@
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--- a/test-data/input/Feature2.bed	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- a/test-data/input/features.header.bed.txt	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-Feature1.bed	ftr1	Feature 1
-Feature2.bed	ftr2	Feature 2
\ No newline at end of file
--- a/test-data/input/regions.header.txt	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-Elements1_regions.bed	elem1	Elements 1
-Elements2_regions.bed	elem2	Elements 2
-Elements3_regions.bed	elem3	Elements 3
-Controls_regions.bed	control	Controls
\ No newline at end of file
Binary file test-data/output_loadandplot/iwtomics.loadandplot.RData has changed
--- a/test-data/output_loadandplot/iwtomics.loadandplot.features.txt	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-ftr1	ftr2
Binary file test-data/output_loadandplot/iwtomics.loadandplot.pdf has changed
--- a/test-data/output_loadandplot/iwtomics.loadandplot.regions.txt	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-control	elem1	elem2	elem3
--- a/test-data/output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-Test: elem1 vs control, on feature ftr1
-Scale 10	0.337	0.492	0.718	0.884	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.886	0.817	0.813	0.839	0.889	0.947	0.983	0.97	0.97	0.935	0.777	0.554	0.362	0.457	0.681	0.84	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.852	0.752	0.691	0.802	0.905	0.995	0.995	0.937	0.817	0.688
-
-Test: elem1 vs control, on feature ftr2
-Scale 20	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-
-Test: elem2 vs control, on feature ftr1
-Scale 50	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-
-Test: elem2 vs control, on feature ftr2
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-
-Test: elem3 vs control, on feature ftr1
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-
-Test: elem3 vs control, on feature ftr2
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-
Binary file test-data/output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf has changed
Binary file test-data/output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf has changed
Binary file test-data/output_testandplot/iwtomics.testandplot.RData has changed
--- a/test-data/output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,312 +0,0 @@
-Test: elem1 vs control, on feature ftr1
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-Scale 25	0.706	0.806	0.903	0.945	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.983	0.97	0.97	0.954	0.943	0.863	0.741	0.67	0.787	0.855	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.867	0.867	0.867	0.867	0.905	0.995	0.995	0.937	0.867	0.827
-Scale 24	0.683	0.806	0.903	0.945	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.983	0.97	0.97	0.954	0.943	0.863	0.741	0.67	0.787	0.855	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.867	0.867	0.867	0.867	0.905	0.995	0.995	0.937	0.867	0.827
-Scale 23	0.656	0.794	0.903	0.945	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.983	0.97	0.97	0.954	0.943	0.863	0.717	0.67	0.787	0.855	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.867	0.867	0.867	0.867	0.905	0.995	0.995	0.937	0.867	0.827
-Scale 22	0.618	0.775	0.891	0.945	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.983	0.97	0.97	0.954	0.943	0.844	0.689	0.67	0.787	0.855	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.867	0.867	0.867	0.867	0.905	0.995	0.995	0.937	0.867	0.827
-Scale 21	0.573	0.742	0.875	0.936	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.983	0.97	0.97	0.954	0.941	0.823	0.66	0.67	0.787	0.855	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.867	0.867	0.867	0.867	0.905	0.995	0.995	0.937	0.867	0.827
-Scale 20	0.538	0.711	0.848	0.924	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.983	0.97	0.97	0.952	0.917	0.802	0.643	0.648	0.787	0.855	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.867	0.867	0.867	0.867	0.905	0.995	0.995	0.937	0.867	0.827
-Scale 19	0.517	0.671	0.814	0.908	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.944	0.944	0.944	0.944	0.944	0.947	0.983	0.97	0.97	0.937	0.897	0.792	0.603	0.605	0.778	0.855	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.867	0.867	0.867	0.867	0.905	0.995	0.995	0.937	0.867	0.827
-Scale 18	0.508	0.648	0.804	0.897	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.933	0.933	0.933	0.933	0.933	0.947	0.983	0.97	0.97	0.935	0.889	0.776	0.561	0.56	0.757	0.844	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.867	0.867	0.867	0.867	0.905	0.995	0.995	0.937	0.867	0.801
-Scale 17	0.502	0.646	0.804	0.897	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.923	0.923	0.923	0.923	0.923	0.947	0.983	0.97	0.97	0.935	0.874	0.735	0.528	0.534	0.717	0.84	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.859	0.859	0.859	0.859	0.905	0.995	0.995	0.937	0.849	0.777
-Scale 16	0.502	0.646	0.804	0.897	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.914	0.913	0.913	0.913	0.913	0.947	0.983	0.97	0.97	0.935	0.849	0.697	0.49	0.533	0.715	0.84	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.852	0.84	0.84	0.84	0.905	0.995	0.995	0.937	0.817	0.747
-Scale 15	0.495	0.646	0.804	0.897	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.914	0.899	0.899	0.899	0.899	0.947	0.983	0.97	0.97	0.935	0.824	0.666	0.442	0.533	0.715	0.84	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.852	0.809	0.809	0.809	0.905	0.995	0.995	0.937	0.817	0.717
-Scale 14	0.474	0.645	0.804	0.897	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.914	0.887	0.883	0.883	0.889	0.947	0.983	0.97	0.97	0.935	0.797	0.615	0.414	0.533	0.715	0.84	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.852	0.792	0.776	0.802	0.905	0.995	0.995	0.937	0.817	0.688
-Scale 13	0.446	0.628	0.804	0.897	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.914	0.887	0.854	0.854	0.889	0.947	0.983	0.97	0.97	0.935	0.777	0.583	0.391	0.533	0.715	0.84	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.852	0.792	0.745	0.802	0.905	0.995	0.995	0.937	0.817	0.688
-Scale 12	0.403	0.586	0.792	0.897	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.914	0.887	0.823	0.839	0.889	0.947	0.983	0.97	0.97	0.935	0.777	0.568	0.381	0.519	0.715	0.84	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.852	0.792	0.745	0.802	0.905	0.995	0.995	0.937	0.817	0.688
-Scale 11	0.368	0.535	0.769	0.897	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.913	0.846	0.813	0.839	0.889	0.947	0.983	0.97	0.97	0.935	0.777	0.558	0.374	0.486	0.715	0.84	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.852	0.792	0.714	0.802	0.905	0.995	0.995	0.937	0.817	0.688
-Scale 10	0.337	0.492	0.718	0.884	0.954	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.948	0.886	0.817	0.813	0.839	0.889	0.947	0.983	0.97	0.97	0.935	0.777	0.554	0.362	0.457	0.681	0.84	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.852	0.752	0.691	0.802	0.905	0.995	0.995	0.937	0.817	0.688
-Scale 9	0.303	0.448	0.659	0.859	0.952	0.966	0.966	0.966	0.966	0.979	0.979	0.979	0.979	0.966	0.936	0.857	0.81	0.813	0.839	0.889	0.947	0.983	0.97	0.97	0.935	0.777	0.54	0.352	0.439	0.632	0.819	0.904	0.904	0.904	0.904	0.904	0.884	0.884	0.889	0.884	0.822	0.699	0.691	0.802	0.905	0.995	0.995	0.937	0.817	0.688
-Scale 8	0.267	0.405	0.616	0.824	0.931	0.958	0.958	0.958	0.958	0.979	0.979	0.979	0.979	0.958	0.914	0.854	0.781	0.813	0.839	0.889	0.947	0.983	0.97	0.97	0.935	0.777	0.53	0.329	0.413	0.63	0.799	0.904	0.904	0.904	0.904	0.904	0.865	0.865	0.889	0.865	0.768	0.656	0.691	0.802	0.905	0.995	0.995	0.937	0.817	0.688
-Scale 7	0.241	0.359	0.555	0.762	0.901	0.938	0.94	0.941	0.956	0.979	0.979	0.979	0.979	0.958	0.91	0.839	0.714	0.782	0.839	0.889	0.947	0.983	0.97	0.97	0.935	0.777	0.503	0.267	0.364	0.629	0.799	0.904	0.904	0.904	0.904	0.904	0.839	0.839	0.889	0.814	0.728	0.604	0.691	0.802	0.905	0.995	0.995	0.937	0.817	0.688
-Scale 6	0.213	0.334	0.502	0.707	0.854	0.909	0.914	0.925	0.956	0.979	0.979	0.979	0.979	0.958	0.9	0.774	0.653	0.731	0.826	0.889	0.947	0.983	0.97	0.97	0.935	0.777	0.449	0.206	0.31	0.569	0.799	0.904	0.904	0.904	0.904	0.904	0.824	0.786	0.889	0.776	0.658	0.523	0.69	0.802	0.905	0.995	0.995	0.937	0.817	0.688
-Scale 5	0.175	0.298	0.446	0.666	0.805	0.909	0.871	0.895	0.952	0.979	0.979	0.979	0.979	0.958	0.852	0.71	0.583	0.662	0.772	0.878	0.947	0.983	0.97	0.97	0.935	0.713	0.35	0.145	0.245	0.483	0.766	0.904	0.904	0.904	0.904	0.904	0.792	0.743	0.889	0.74	0.592	0.512	0.588	0.802	0.905	0.995	0.995	0.937	0.817	0.638
-Scale 4	0.138	0.246	0.4	0.606	0.785	0.909	0.871	0.831	0.924	0.979	0.979	0.979	0.979	0.929	0.796	0.631	0.483	0.556	0.709	0.831	0.947	0.983	0.97	0.97	0.934	0.62	0.25	0.098	0.195	0.398	0.688	0.89	0.898	0.898	0.898	0.883	0.725	0.68	0.889	0.74	0.588	0.477	0.485	0.736	0.905	0.995	0.995	0.937	0.792	0.558
-Scale 3	0.114	0.18	0.343	0.538	0.785	0.909	0.871	0.805	0.88	0.958	0.963	0.963	0.965	0.885	0.702	0.525	0.412	0.424	0.591	0.774	0.911	0.983	0.97	0.97	0.894	0.488	0.166	0.065	0.128	0.314	0.612	0.83	0.898	0.898	0.898	0.816	0.669	0.68	0.889	0.74	0.585	0.382	0.399	0.608	0.898	0.995	0.995	0.937	0.71	0.498
-Scale 2	0.099	0.133	0.263	0.459	0.698	0.909	0.871	0.672	0.794	0.95	0.95	0.94	0.965	0.821	0.583	0.438	0.362	0.36	0.454	0.658	0.869	0.983	0.934	0.934	0.83	0.348	0.108	0.049	0.088	0.231	0.478	0.816	0.888	0.823	0.858	0.813	0.537	0.634	0.889	0.74	0.454	0.312	0.316	0.485	0.786	0.995	0.995	0.868	0.61	0.44
-Scale 1	0.098	0.112	0.189	0.366	0.592	0.909	0.732	0.564	0.649	0.921	0.848	0.82	0.965	0.675	0.483	0.386	0.359	0.345	0.362	0.506	0.745	0.983	0.841	0.93	0.651	0.207	0.065	0.046	0.058	0.152	0.368	0.682	0.888	0.683	0.858	0.718	0.43	0.487	0.889	0.604	0.351	0.277	0.265	0.377	0.62	0.942	0.989	0.749	0.509	0.387
-
-Test: elem1 vs control, on feature ftr2
-Scale 50	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 49	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 48	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 47	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 46	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 45	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 44	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 43	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 42	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 41	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 40	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 39	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 38	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 37	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 36	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 35	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 34	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 33	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 32	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 31	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 30	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 29	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 28	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 27	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 26	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 25	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 24	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 23	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 22	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 21	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 20	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 19	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 18	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 17	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 16	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 15	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 14	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 13	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 12	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 11	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 10	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 9	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 8	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 7	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 6	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 5	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 4	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 3	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 2	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 1	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-
-Test: elem2 vs control, on feature ftr1
-Scale 50	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 49	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 48	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 47	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 46	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 45	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 44	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 43	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 42	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 41	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 40	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 39	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 38	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 37	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 36	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 35	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 34	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 33	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 32	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 31	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 30	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 29	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 28	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 27	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 26	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 25	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 24	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 23	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 22	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 21	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 20	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 19	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 18	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 17	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 16	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 15	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 14	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 13	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 12	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 11	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 10	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 9	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 8	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 7	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 6	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 5	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 4	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 3	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 2	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 1	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-
-Test: elem2 vs control, on feature ftr2
-Scale 50	0.989	0.937	0.845	0.825	0.825	0.825	0.825	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 49	0.989	0.937	0.845	0.797	0.797	0.797	0.797	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 48	0.989	0.937	0.845	0.772	0.772	0.772	0.795	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 47	0.989	0.937	0.845	0.759	0.755	0.761	0.795	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 46	0.989	0.937	0.845	0.759	0.755	0.761	0.795	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 45	0.989	0.937	0.845	0.759	0.712	0.761	0.795	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 44	0.989	0.937	0.845	0.759	0.696	0.715	0.795	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 43	0.989	0.937	0.845	0.759	0.683	0.683	0.744	0.828	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 42	0.989	0.937	0.845	0.759	0.68	0.68	0.712	0.787	0.852	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 41	0.989	0.937	0.845	0.759	0.68	0.68	0.686	0.759	0.821	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.864	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 40	0.989	0.937	0.845	0.759	0.673	0.673	0.673	0.734	0.79	0.834	0.852	0.852	0.852	0.852	0.852	0.852	0.852	0.852	0.852	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 39	0.989	0.937	0.845	0.759	0.65	0.65	0.652	0.718	0.767	0.804	0.827	0.841	0.841	0.841	0.841	0.841	0.841	0.841	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 38	0.989	0.937	0.845	0.759	0.644	0.626	0.639	0.7	0.758	0.802	0.805	0.805	0.834	0.834	0.834	0.834	0.834	0.834	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 37	0.989	0.937	0.845	0.759	0.644	0.605	0.625	0.681	0.739	0.802	0.805	0.801	0.801	0.825	0.825	0.825	0.825	0.825	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 36	0.989	0.937	0.845	0.759	0.644	0.593	0.613	0.678	0.739	0.802	0.805	0.801	0.801	0.819	0.808	0.808	0.808	0.821	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 35	0.989	0.937	0.845	0.759	0.644	0.582	0.613	0.678	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.789	0.794	0.821	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 34	0.989	0.937	0.845	0.759	0.644	0.579	0.61	0.678	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.745	0.794	0.821	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 33	0.989	0.937	0.845	0.759	0.644	0.579	0.593	0.675	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.733	0.751	0.821	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 32	0.989	0.937	0.845	0.759	0.644	0.577	0.577	0.659	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.733	0.733	0.782	0.849	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 31	0.989	0.937	0.845	0.759	0.644	0.55	0.55	0.622	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.733	0.733	0.752	0.811	0.874	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 30	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.609	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.715	0.715	0.727	0.784	0.84	0.918	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 29	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.585	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.69	0.706	0.763	0.816	0.889	0.947	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 28	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.678	0.692	0.748	0.798	0.864	0.925	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.965	0.954	0.954	0.954	0.954	0.98	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954	0.954
-Scale 27	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.667	0.675	0.727	0.782	0.851	0.908	0.934	0.948	0.948	0.952	0.952	0.952	0.952	0.952	0.965	0.952	0.952	0.952	0.952	0.98	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952
-Scale 26	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.642	0.662	0.708	0.769	0.846	0.899	0.918	0.927	0.946	0.952	0.952	0.952	0.952	0.952	0.965	0.952	0.952	0.952	0.952	0.98	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952
-Scale 25	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.626	0.662	0.708	0.757	0.829	0.899	0.918	0.918	0.926	0.952	0.952	0.952	0.952	0.952	0.965	0.952	0.952	0.952	0.952	0.98	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952	0.952
-Scale 24	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.622	0.662	0.708	0.757	0.829	0.899	0.918	0.918	0.918	0.93	0.948	0.948	0.948	0.948	0.965	0.948	0.948	0.948	0.948	0.98	0.948	0.948	0.948	0.948	0.948	0.948	0.948	0.948	0.948	0.948	0.948	0.948	0.948	0.948
-Scale 23	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.622	0.658	0.708	0.757	0.829	0.899	0.918	0.918	0.918	0.918	0.929	0.947	0.947	0.947	0.965	0.947	0.947	0.947	0.947	0.98	0.947	0.947	0.947	0.947	0.947	0.947	0.947	0.947	0.947	0.947	0.947	0.947	0.947	0.947
-Scale 22	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.644	0.708	0.757	0.829	0.899	0.918	0.918	0.918	0.918	0.926	0.926	0.941	0.941	0.965	0.941	0.941	0.941	0.941	0.98	0.941	0.941	0.941	0.941	0.941	0.941	0.941	0.941	0.941	0.941	0.941	0.941	0.941	0.941
-Scale 21	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.603	0.681	0.757	0.829	0.899	0.918	0.918	0.918	0.918	0.926	0.926	0.926	0.937	0.965	0.937	0.937	0.937	0.937	0.98	0.937	0.937	0.937	0.937	0.937	0.937	0.937	0.937	0.937	0.937	0.937	0.937	0.937	0.937
-Scale 20	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.561	0.653	0.733	0.829	0.899	0.918	0.918	0.918	0.918	0.926	0.926	0.926	0.926	0.965	0.926	0.922	0.922	0.922	0.98	0.922	0.922	0.922	0.922	0.922	0.922	0.922	0.929	0.922	0.922	0.922	0.922	0.922	0.922
-Scale 19	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.541	0.617	0.706	0.82	0.899	0.918	0.918	0.918	0.918	0.926	0.926	0.926	0.926	0.965	0.926	0.918	0.918	0.918	0.98	0.918	0.918	0.918	0.912	0.903	0.903	0.903	0.929	0.903	0.903	0.903	0.903	0.903	0.903
-Scale 18	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.517	0.591	0.669	0.799	0.898	0.918	0.918	0.918	0.918	0.926	0.926	0.926	0.926	0.965	0.926	0.918	0.918	0.918	0.98	0.918	0.918	0.918	0.912	0.899	0.899	0.899	0.929	0.899	0.899	0.899	0.899	0.899	0.899
-Scale 17	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.517	0.561	0.635	0.766	0.88	0.918	0.918	0.918	0.918	0.926	0.926	0.926	0.926	0.965	0.926	0.918	0.918	0.918	0.98	0.918	0.918	0.918	0.904	0.899	0.899	0.899	0.929	0.899	0.899	0.899	0.899	0.899	0.899
-Scale 16	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.517	0.548	0.621	0.732	0.866	0.907	0.907	0.907	0.913	0.926	0.926	0.926	0.926	0.965	0.926	0.907	0.907	0.907	0.98	0.907	0.907	0.904	0.904	0.899	0.899	0.899	0.929	0.899	0.899	0.899	0.899	0.899	0.899
-Scale 15	0.989	0.937	0.845	0.759	0.644	0.545	0.545	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.517	0.547	0.621	0.721	0.849	0.898	0.898	0.898	0.913	0.926	0.926	0.926	0.926	0.965	0.926	0.904	0.904	0.904	0.98	0.904	0.904	0.904	0.904	0.899	0.899	0.899	0.929	0.899	0.899	0.899	0.899	0.899	0.899
-Scale 14	0.989	0.937	0.845	0.759	0.644	0.508	0.508	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.517	0.541	0.621	0.721	0.849	0.898	0.898	0.898	0.913	0.926	0.926	0.926	0.926	0.965	0.926	0.903	0.903	0.903	0.98	0.903	0.903	0.903	0.896	0.885	0.885	0.89	0.929	0.89	0.89	0.89	0.89	0.89	0.89
-Scale 13	0.989	0.937	0.845	0.759	0.644	0.5	0.467	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.517	0.504	0.618	0.721	0.849	0.898	0.898	0.898	0.913	0.926	0.926	0.926	0.926	0.965	0.926	0.902	0.902	0.902	0.98	0.902	0.902	0.902	0.88	0.88	0.88	0.89	0.929	0.89	0.89	0.89	0.89	0.89	0.89
-Scale 12	0.989	0.937	0.845	0.759	0.644	0.5	0.444	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.517	0.436	0.575	0.721	0.849	0.898	0.898	0.898	0.913	0.926	0.926	0.926	0.926	0.965	0.926	0.889	0.889	0.889	0.98	0.889	0.889	0.881	0.869	0.864	0.864	0.89	0.929	0.89	0.89	0.89	0.89	0.89	0.89
-Scale 11	0.989	0.937	0.845	0.759	0.644	0.5	0.435	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.517	0.435	0.498	0.679	0.849	0.898	0.898	0.898	0.913	0.926	0.926	0.926	0.926	0.965	0.926	0.883	0.877	0.877	0.98	0.877	0.874	0.868	0.857	0.84	0.849	0.89	0.929	0.89	0.89	0.89	0.89	0.89	0.89
-Scale 10	0.989	0.937	0.845	0.759	0.644	0.5	0.435	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.517	0.435	0.434	0.611	0.821	0.898	0.898	0.898	0.913	0.926	0.926	0.926	0.926	0.965	0.926	0.881	0.858	0.858	0.98	0.858	0.858	0.854	0.815	0.831	0.849	0.89	0.929	0.89	0.89	0.89	0.89	0.89	0.89
-Scale 9	0.989	0.937	0.845	0.759	0.644	0.5	0.435	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.517	0.394	0.382	0.535	0.762	0.894	0.868	0.872	0.913	0.926	0.926	0.926	0.926	0.965	0.926	0.881	0.834	0.834	0.98	0.834	0.834	0.812	0.767	0.765	0.849	0.89	0.929	0.89	0.89	0.89	0.89	0.89	0.89
-Scale 8	0.989	0.937	0.845	0.759	0.644	0.5	0.404	0.583	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.598	0.45	0.336	0.347	0.468	0.686	0.894	0.841	0.872	0.913	0.926	0.926	0.926	0.926	0.965	0.926	0.881	0.819	0.807	0.98	0.807	0.784	0.784	0.767	0.696	0.783	0.89	0.929	0.89	0.89	0.89	0.89	0.89	0.89
-Scale 7	0.989	0.937	0.845	0.759	0.644	0.5	0.404	0.541	0.739	0.802	0.805	0.801	0.801	0.819	0.801	0.696	0.52	0.383	0.302	0.319	0.421	0.612	0.894	0.777	0.844	0.913	0.926	0.926	0.926	0.926	0.965	0.926	0.881	0.783	0.77	0.98	0.784	0.784	0.784	0.767	0.696	0.719	0.849	0.929	0.88	0.88	0.88	0.88	0.88	0.88
-Scale 6	0.989	0.937	0.845	0.759	0.644	0.5	0.303	0.434	0.718	0.802	0.805	0.801	0.801	0.819	0.801	0.649	0.446	0.343	0.254	0.301	0.387	0.545	0.894	0.703	0.781	0.892	0.926	0.926	0.926	0.926	0.965	0.926	0.85	0.755	0.765	0.98	0.784	0.784	0.784	0.767	0.69	0.668	0.797	0.929	0.877	0.837	0.837	0.837	0.837	0.859
-Scale 5	0.989	0.937	0.845	0.759	0.644	0.391	0.216	0.376	0.637	0.802	0.805	0.791	0.791	0.819	0.747	0.558	0.417	0.297	0.168	0.264	0.369	0.509	0.894	0.674	0.696	0.834	0.917	0.917	0.917	0.917	0.965	0.91	0.822	0.702	0.765	0.98	0.784	0.784	0.784	0.767	0.641	0.629	0.772	0.929	0.877	0.832	0.81	0.81	0.81	0.859
-Scale 4	0.989	0.937	0.845	0.759	0.506	0.28	0.169	0.331	0.581	0.802	0.805	0.745	0.735	0.819	0.736	0.529	0.37	0.189	0.104	0.204	0.348	0.509	0.894	0.674	0.599	0.778	0.862	0.893	0.896	0.897	0.965	0.897	0.807	0.618	0.738	0.98	0.784	0.784	0.784	0.699	0.595	0.564	0.769	0.929	0.877	0.832	0.798	0.782	0.804	0.859
-Scale 3	0.989	0.937	0.845	0.633	0.388	0.219	0.13	0.241	0.539	0.802	0.805	0.745	0.663	0.819	0.736	0.519	0.234	0.092	0.104	0.11	0.283	0.509	0.894	0.674	0.557	0.688	0.829	0.831	0.879	0.897	0.965	0.897	0.727	0.483	0.71	0.98	0.783	0.745	0.712	0.644	0.547	0.488	0.755	0.929	0.877	0.832	0.7	0.777	0.804	0.859
-Scale 2	0.989	0.937	0.744	0.473	0.298	0.174	0.09	0.149	0.429	0.802	0.805	0.658	0.644	0.819	0.736	0.389	0.109	0.092	0.104	0.086	0.152	0.478	0.894	0.674	0.472	0.55	0.776	0.789	0.789	0.883	0.965	0.894	0.574	0.353	0.626	0.98	0.783	0.651	0.64	0.612	0.487	0.405	0.651	0.929	0.877	0.698	0.624	0.7	0.804	0.859
-Scale 1	0.989	0.84	0.607	0.379	0.238	0.129	0.069	0.09	0.274	0.694	0.805	0.506	0.532	0.819	0.648	0.188	0.076	0.091	0.104	0.082	0.087	0.295	0.894	0.555	0.389	0.468	0.655	0.729	0.735	0.785	0.965	0.75	0.415	0.284	0.443	0.98	0.657	0.612	0.64	0.575	0.395	0.346	0.507	0.929	0.716	0.614	0.579	0.615	0.743	0.859
-
-Test: elem3 vs control, on feature ftr1
-Scale 50	0.756	0.756	0.644	0.644	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.117	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.186	0.698	0.885	0.732	0.602	0.474	0.381	0.381	0.455	0.607	0.822	0.822	0.689
-Scale 49	0.756	0.756	0.644	0.644	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.117	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.186	0.698	0.885	0.732	0.602	0.474	0.381	0.381	0.455	0.607	0.822	0.822	0.689
-Scale 48	0.756	0.756	0.644	0.644	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.117	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.186	0.698	0.885	0.732	0.602	0.474	0.381	0.381	0.455	0.607	0.822	0.822	0.689
-Scale 47	0.756	0.756	0.644	0.644	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.117	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.186	0.698	0.885	0.732	0.602	0.474	0.381	0.381	0.455	0.607	0.822	0.822	0.689
-Scale 46	0.756	0.756	0.644	0.644	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.117	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.186	0.698	0.885	0.732	0.602	0.474	0.381	0.381	0.455	0.607	0.822	0.822	0.689
-Scale 45	0.756	0.756	0.644	0.644	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.117	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.186	0.698	0.885	0.732	0.602	0.474	0.381	0.381	0.455	0.607	0.822	0.822	0.689
-Scale 44	0.756	0.756	0.644	0.644	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.117	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.186	0.698	0.885	0.732	0.602	0.474	0.381	0.381	0.455	0.607	0.822	0.822	0.689
-Scale 43	0.756	0.756	0.644	0.644	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.117	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.186	0.698	0.885	0.732	0.602	0.474	0.381	0.381	0.455	0.607	0.822	0.822	0.689
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-Scale 7	0.756	0.756	0.552	0.548	0.662	0.823	0.943	1	0.986	0.927	0.806	0.488	0.056	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.122	0.698	0.885	0.732	0.602	0.474	0.36	0.348	0.455	0.607	0.822	0.822	0.689
-Scale 6	0.756	0.756	0.552	0.499	0.662	0.823	0.943	1	0.986	0.927	0.806	0.472	0.035	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.121	0.698	0.885	0.732	0.602	0.474	0.36	0.348	0.455	0.607	0.822	0.822	0.689
-Scale 5	0.756	0.756	0.552	0.431	0.611	0.823	0.943	1	0.986	0.927	0.806	0.404	0.019	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.121	0.698	0.885	0.732	0.602	0.474	0.307	0.298	0.455	0.607	0.822	0.822	0.689
-Scale 4	0.756	0.756	0.552	0.414	0.527	0.795	0.943	1	0.986	0.927	0.758	0.323	0.011	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.094	0.698	0.885	0.732	0.602	0.416	0.24	0.218	0.411	0.607	0.822	0.822	0.689
-Scale 3	0.756	0.756	0.552	0.328	0.439	0.722	0.943	1	0.986	0.902	0.672	0.242	0.006	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.057	0.698	0.885	0.732	0.538	0.325	0.186	0.149	0.294	0.597	0.822	0.822	0.689
-Scale 2	0.756	0.756	0.461	0.237	0.32	0.607	0.906	1	0.986	0.826	0.543	0.164	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.034	0.688	0.885	0.732	0.424	0.263	0.151	0.11	0.205	0.478	0.822	0.822	0.598
-Scale 1	0.753	0.699	0.315	0.187	0.228	0.455	0.803	1	0.935	0.698	0.387	0.071	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.007	0.546	0.885	0.578	0.334	0.195	0.122	0.096	0.13	0.319	0.767	0.783	0.496
-
-Test: elem3 vs control, on feature ftr2
-Scale 50	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 49	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 48	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 47	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 46	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 45	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 44	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 43	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 42	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 41	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 40	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 39	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 38	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 37	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 36	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 35	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 34	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 33	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 32	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 31	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 30	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 29	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 28	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 27	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 26	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 25	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 24	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.276	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 23	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.826	0.229	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 22	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.908	0.908	0.908	0.908	0.8	0.21	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 21	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.906	0.906	0.9	0.792	0.193	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 20	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.9	0.9	0.9	0.792	0.181	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 19	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.9	0.9	0.9	0.792	0.165	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 18	0.914	0.914	0.914	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.9	0.9	0.9	0.78	0.142	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 17	0.907	0.907	0.907	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.899	0.899	0.89	0.742	0.129	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 16	0.881	0.891	0.892	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.896	0.891	0.865	0.709	0.122	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 15	0.861	0.861	0.892	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.907	0.885	0.861	0.849	0.701	0.113	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 14	0.853	0.853	0.859	0.917	0.925	0.949	0.925	0.925	0.925	0.925	0.941	0.941	0.925	0.925	0.925	0.925	0.925	0.925	0.892	0.854	0.844	0.844	0.691	0.105	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 13	0.852	0.852	0.852	0.882	0.923	0.949	0.923	0.923	0.923	0.923	0.941	0.941	0.923	0.923	0.923	0.923	0.923	0.92	0.871	0.841	0.841	0.835	0.654	0.092	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 12	0.837	0.837	0.837	0.863	0.898	0.949	0.915	0.915	0.915	0.915	0.941	0.941	0.915	0.915	0.915	0.915	0.915	0.893	0.853	0.832	0.832	0.819	0.603	0.078	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 11	0.81	0.81	0.82	0.853	0.883	0.949	0.89	0.89	0.89	0.89	0.941	0.941	0.89	0.89	0.89	0.89	0.895	0.878	0.842	0.818	0.813	0.774	0.562	0.07	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 10	0.778	0.778	0.802	0.838	0.883	0.949	0.883	0.883	0.883	0.883	0.941	0.941	0.883	0.88	0.88	0.88	0.895	0.878	0.839	0.798	0.756	0.732	0.528	0.064	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 9	0.743	0.743	0.763	0.827	0.883	0.949	0.883	0.883	0.883	0.883	0.941	0.941	0.883	0.88	0.88	0.88	0.895	0.878	0.805	0.737	0.708	0.708	0.517	0.051	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 8	0.724	0.724	0.724	0.782	0.866	0.949	0.875	0.875	0.875	0.88	0.941	0.941	0.88	0.88	0.88	0.88	0.895	0.858	0.75	0.697	0.697	0.697	0.499	0.038	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 7	0.71	0.71	0.71	0.731	0.826	0.949	0.861	0.861	0.861	0.88	0.941	0.941	0.863	0.863	0.863	0.863	0.895	0.801	0.695	0.685	0.685	0.685	0.436	0.029	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 6	0.681	0.671	0.671	0.695	0.78	0.949	0.823	0.823	0.823	0.88	0.941	0.941	0.859	0.82	0.82	0.824	0.895	0.74	0.667	0.667	0.667	0.632	0.349	0.023	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 5	0.681	0.622	0.63	0.669	0.759	0.949	0.822	0.767	0.813	0.88	0.941	0.941	0.859	0.801	0.756	0.824	0.895	0.74	0.653	0.634	0.608	0.545	0.306	0.015	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 4	0.681	0.622	0.588	0.655	0.759	0.949	0.822	0.734	0.787	0.88	0.941	0.941	0.859	0.773	0.738	0.824	0.895	0.74	0.638	0.569	0.564	0.545	0.278	0.009	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 3	0.681	0.622	0.588	0.599	0.759	0.949	0.822	0.726	0.706	0.88	0.941	0.941	0.859	0.672	0.738	0.824	0.895	0.74	0.567	0.512	0.564	0.545	0.234	0.006	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 2	0.681	0.622	0.5	0.5	0.717	0.949	0.822	0.578	0.586	0.784	0.941	0.941	0.759	0.534	0.611	0.824	0.895	0.662	0.45	0.47	0.564	0.545	0.158	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-Scale 1	0.681	0.553	0.434	0.417	0.582	0.949	0.66	0.476	0.513	0.664	0.889	0.868	0.592	0.461	0.487	0.708	0.895	0.512	0.342	0.402	0.564	0.494	0.074	0.002	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001	0.001
-
Binary file test-data/output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf has changed
--- a/test-data/output_testandplot/iwtomics.testandplot.selectedfeatures.txt	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-ftr1	ftr2
Binary file test-data/output_testandplot/iwtomics.testandplot.summaryplot.pdf has changed
--- a/test-data/output_testandplot/iwtomics.testandplot.tests.txt	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-elem1 vs control	elem2 vs control	elem3 vs control
--- a/testandplot.R	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
-  args=commandArgs(TRUE)
-  
-  # get args names and values
-  args_values=strsplit(args,'=')
-  args_names=unlist(lapply(args_values,function(arg) arg[1]))
-  names(args_values)=args_names
-  args_values=lapply(args_values,function(arg) arg[2])
-  # read filenames
-  adjustedpvaluematrix=args_values$adjustedpvaluematrix
-  iwtomicsrespdf=args_values$iwtomicsrespdf
-  iwtomicssumpdf=args_values$iwtomicssumpdf
-  regionids=args_values$regionids
-  featureids=args_values$featureids
-  rdatafile=args_values$rdatafile
-  iwtomicsrdata=args_values$iwtomicsrdata
-  iwtomicstests=args_values$iwtomicstests
-  iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
-  # read parameters (from region1 on)
-  i_region1=which(args_names=='region1')
-  for(i in i_region1:length(args)){
-    eval(parse(text=args[[i]]))
-  }
-  
-  # load RData
-  load(rdatafile)
-  # read regionids and featureids
-  regionids=as.character(read.delim(regionids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
-  featureids=as.character(read.delim(featureids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
-  # retrieve region1, region2 and features_subset ids and check they are in the RData
-  id_region1=regionids[region1]
-  id_region2=regionids[region2]
-  id_features_subset=featureids[features_subset]
-  if(length(setdiff(c(id_region1,id_region2),idRegions(regionsFeatures)))!=0){
-    write("Wrong region ids.", stderr())
-    quit(save="no", status=10)
-  }
-  if(length(setdiff(id_features_subset,idFeatures(regionsFeatures)))!=0){
-    write("Wrong feature ids.", stderr())
-    quit(save="no", status=20)
-  }
-  if(sum(duplicated(paste0(id_region1,id_region2)))){
-    write("Same test repeated multiple times.", stderr())
-    quit(save="no", status=30)
-  }
-  
-  # perform test
-  tryCatch({
-    # fix repeated probs
-    if(statistics=='quantile'){
-      # fix repeated probs
-      testprobs=sort(unique(testprobs))
-    }else{
-      testprobs=0.5
-    }
-    regionsFeatures_test=IWTomicsTest(regionsFeatures,id_region1,id_region2,id_features_subset,
-                                      statistics=statistics,probs=testprobs,B=B)
-    # create adjustedvaluematrix output
-    for(test in seq_along(id_region1)){
-      for(id_feature in id_features_subset){
-        write(paste0('Test: ',id_region1[test],' vs ',id_region2[test],', on feature ',id_feature),
-              file=adjustedpvaluematrix,append=TRUE,sep='\t')
-        pval=regionsFeatures_test@test$result[[test]][[id_feature]]$adjusted_pval_matrix
-        row.names(pval)=paste('Scale',rev(seq_len(nrow(pval))))
-        write.table(pval,file=adjustedpvaluematrix,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
-        write('',file=adjustedpvaluematrix,append=TRUE,sep='\t')
-      }
-    }
-  }, error = function(err) {
-    write("Testing error.", stderr())
-    quit(save="no", status=40) #error testing
-  })
-  
-  # plot test results
-  pdf(iwtomicsrespdf,width=5,height=7)
-  if(plottype=='boxplot'){
-    # fix repeated probs
-    probs=sort(unique(probs))
-  }else{
-    probs=c(0.25,0.5,0.75)
-  }
-  plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
-  dev.off()
-  
-  # plot summary results
-  if(groupby!='none'){
-    pdf(iwtomicssumpdf,width=15,height=10)
-    plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,ask=FALSE,append=TRUE)
-    dev.off()
-  }
-  
-  # create output
-  write.table(as.data.frame(t(paste(id_region1,'vs',id_region2))),file=iwtomicstests,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
-  write.table(as.data.frame(t(idFeatures(regionsFeatures_test))),file=iwtomicsselectedfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
-  save(regionsFeatures_test,file=iwtomicsrdata)
-}else{
-  write("Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
-  quit(save="no", status=255)
-}
\ No newline at end of file
--- a/testandplot.xml	Tue Jun 20 13:14:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,201 +0,0 @@
-<tool id="iwtomics_testandplot" name="IWTomics Test" version="@VERSION@.0">
-  <description>and Plot</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements" />
-
-  <command detect_errors="exit_code">
-<![CDATA[
-    Rscript '$__tool_directory__/testandplot.R' adjustedpvaluematrix='${adjustedpvaluematrix}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' iwtomicsrdata='${iwtomicsrdata}' iwtomicstests='${iwtomicstests}' iwtomicsselectedfeatures='${iwtomicsselectedfeatures}'
-      regionids='${regionids}'
-      featureids='${featureids}'
-      rdatafile='${rdata}'
-
-      #set region1 = ','.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
-      #set region2 = ','.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
-      region1='c(${region1})'
-      region2='c(${region2})'
-
-      features_subset='c(${featureslist})'
-
-      statistics="'${conditionalstatistics.statistics}'"
-      #if $conditionalstatistics.statistics == "quantile":
-        #set probabilities = ','.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
-        testprobs='c(${probabilities})'
-      #end if
-
-      B='${permutations}'
-
-      testalpha='${plotres.alpha}'
-      average='${plotres.average}'
-      size='${plotres.size}'
-      plottype="'${plotres.conditionalplottype.plottype}'"
-      #if $plotres.conditionalplottype.plottype == "boxplot":
-        #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
-        #if $probs != "":
-          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
-        #else:
-          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
-        #end if
-      #end if
-
-      groupby="'${plotsum.conditionalgroupby.groupby}'"
-      #if $plotsum.conditionalgroupby.groupby == "test":
-        summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
-        only_significant='${plotsum.conditionalgroupby.testonlysig}'
-      #elif $plotsum.conditionalgroupby.groupby == "feature":
-        summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
-        only_significant='${plotsum.conditionalgroupby.featureonlysig}'
-      #end if
-]]>
-  </command>
-
-  <inputs>
-    <!-- RData -->
-    <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object" help="File created by 'IWTomics Load Smooth and Plot'." />
-    <!-- region IDs -->
-    <param format="tabular" name="regionids" type="data" label="Select region dataset IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
-    <!-- feature IDs -->
-    <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
-
-    <!-- repeat region ids -->
-    <section name="regionssection" title="Select regions for Interval-Wise Testing" expanded="True" help="IDs of the region datasets to be tested.">
-      <repeat name="regions" title="Two-sample test" min="1">
-        <param name="region0" type="data_column" data_ref="regionids" numerical="False" label="Region 1" multiple="False" use_header_names="True" />
-        <param name="region1" type="data_column" data_ref="regionids" numerical="False" label="Region 2" multiple="False" use_header_names="True" />
-      </repeat>
-    </section>
-
-    <!-- feature ids list -->
-    <param name="featureslist" type="data_column" data_ref="featureids" numerical="False" label="Select features" multiple="True" use_header_names="True" help="IDs of the features to be tested." />
-
-    <!-- conditional statistics -->
-    <conditional name="conditionalstatistics">
-      <!-- statistics -->
-      <param name="statistics" type="select" label="Test statistics">
-        <option value="mean">Mean difference</option>
-        <option value="median">Median difference</option>
-        <option value="variance">Variance ratio</option>
-        <option value="quantile">Quantile difference(s)</option>
-      </param>
-      <!-- conditional choice: statistics=quantile -->
-      <when value="quantile">
-        <section name="quantilesection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantiles in test statistics.">
-          <repeat name="qprobabilities" title="Probabilities" min="1">
-            <param name="qprob" size="4" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
-          </repeat>
-        </section>
-      </when>
-    </conditional>
-
-    <!-- permutations -->
-    <param name="permutations" type="integer" value="1000" min="1" label="Number of permutations" />
-
-    <!-- plot IWTomics results -->
-    <section name="plotres" title="Plot IWTomics test results" expanded="True">
-      <!-- alpha -->
-      <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
-      <expand macro="plot-params" />
-    </section>
-
-    <!-- summary plot -->
-    <expand macro="plot-sum" />
-  </inputs>
-
-  <outputs>
-    <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" />
-    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
-    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
-    <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" />
-    <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" />
-    <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" />
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="rdata" value="output_loadandplot/iwtomics.loadandplot.RData" ftype="rdata" />
-      <param name="regionids" value="output_loadandplot/iwtomics.loadandplot.regions.txt" ftype="tabular" />
-      <param name="featureids" value="output_loadandplot/iwtomics.loadandplot.features.txt" ftype="tabular" />
-      <repeat name="regions">
-          <param name="region0" value="2" />
-          <param name="region1" value="1" />
-      </repeat>
-      <repeat name="regions">
-          <param name="region0" value="3" />
-          <param name="region1" value="1" />
-      </repeat>
-      <repeat name="regions">
-          <param name="region0" value="4" />
-          <param name="region1" value="1" />
-      </repeat>
-      <param name="featureslist" value="1,2" />
-      <param name="statistics" value="mean" />
-      <param name="permutations" value="1000" />
-      <param name="alpha" value="0.05" />
-      <param name="average" value="TRUE" />
-      <param name="size" value="TRUE" />
-      <param name="plottype" value="boxplot" />
-      <param name="prob0" value="0.25" />
-      <param name="prob1" value="0.5" />
-      <param name="prob2" value="0.75" />
-      <param name="groupby" value="feature" />
-      <param name="featurealphaplot" value="0.05" />
-      <param name="featureonlysig" value="TRUE" />
-      <output name="adjustedpvaluematrix" file="output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt" compare="sim_size" />
-      <output name="iwtomicsrespdf" file="output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf" compare="sim_size" />
-      <output name="iwtomicssumpdf" file="output_testandplot/iwtomics.testandplot.summaryplot.pdf" compare="sim_size" />
-      <output name="iwtomicsrdata" file="output_testandplot/iwtomics.testandplot.RData" compare="sim_size" />
-      <output name="iwtomicstests" file="output_testandplot/iwtomics.testandplot.tests.txt" />
-      <output name="iwtomicsselectedfeatures" file="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" />
-    </test>
-  </tests>
-
-  <help><![CDATA[
-This tool statistically evaluates differences in genomic features between groups of regions along the genome.
-In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise
-Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation
-tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test
-and all possible scales. Moreover, it creates a graphical representation of the Interval-Wise Testing results
-and a summary plot (optional) with p-values at the maximum scale. The tool *IWTomics Plot with Threshold on Test Scale*
-permits to select the scale to be used in the plots.
-
------
-
-**Input files**
-
-RData file with the IWTomicsData object, tabular files with region dataset IDs and feature IDs.
-These files are created by the tool *IWTomics Load Smooth and Plot*.
-
------
-
-**Output**
-
-The tool returns:
-
-1. TXT file with an adjusted p-value matrix for every test performed. Each matrix contains a p-value curve (row) for every scale considered in the test;
-2. PDF file with the plotted test results;
-3. PDF file with the summary plot;
-4. RData with the IWTomicsData object with the test results;
-5. Test identifiers;
-6. Feature identifiers.
-
-4-6 can be used as input of the tool *IWTomics Plot with Threshold on Test Scale*
-
------
-
-.. class:: infomark
-
-**Notes**
-
-This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
-
-It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
-The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
-
-.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
-  ]]></help>
-
-  <expand macro="citations" />
-
-</tool>