changeset 0:800c7e974e3b draft

planemo upload for repository https://github.com/fabio-cumbo/IWTomics4Galaxy commit 90c984bb9f803e1531fe4cb670e876809d48d205

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/loadandplot.R	Fri Aug 04 17:51:00 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/macros.xml	Fri Aug 04 17:51:00 2017 -0400
@@ -0,0 +1,105 @@
+<macros>
+    <token name="@VERSION@">1.0.0</token>
+    <xml name="requirements">
+        <requirements>
+            <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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotwithscale.R	Fri Aug 04 17:51:00 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/test-data/input/Controls_regions.bed	Fri Aug 04 17:51:00 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
+chr21	16255112	16355112
+chr21	45089115	45189115
+chrX	23898983	23998983
+chrX	37029585	37129585
+chrX	103593349	103693349

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/Elements1_regions.bed	Fri Aug 04 17:51:00 2017 -0400
@@ -0,0 +1,25 @@
+chr2	49960150	50060150
+chr2	55912445	56012445
+chr3	140326750	140426750
+chr4	41772201	41872201
+chr4	70629719	70729719
+chr4	109340735	109440735
+chr5	15025389	15125389
+chr5	43028888	43128888
+chr5	58231354	58331354
+chr5	91277761	91377761
+chr5	119464508	119564508
+chr6	85309170	85409170
+chr6	85762072	85862072
+chr6	134621363	134721363
+chr6	147470164	147570164
+chr7	77195798	77295798
+chr7	77880914	77980914
+chr7	114805399	114905399
+chr10	46350885	46450885
+chr10	67833078	67933078
+chr12	27722692	27822692
+chr12	95518506	95618506
+chr12	117863466	117963466
+chr14	100464166	100564166
+chrX	29266748	29366748

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/Elements2_regions.bed	Fri Aug 04 17:51:00 2017 -0400
@@ -0,0 +1,20 @@
+chr1	65942901	66042901
+chr1	117128102	117228102
+chr1	190338169	190438169
+chr2	227365478	227465478
+chr6	50856764	50956764
+chr6	135703067	135803067
+chr7	38228726	38328726
+chr7	51115898	51215898
+chr7	150325760	150425760
+chr8	25475691	25575691
+chr9	73374609	73474609
+chr11	55092625	55192625
+chr11	86581661	86681661
+chr12	12795284	12895284
+chr12	48151882	48251882
+chr12	83109951	83209951
+chr15	31430278	31530278
+chr15	65610815	65710815
+chr17	40766223	40866223
+chr20	17245048	17345048

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/Elements3_regions.bed	Fri Aug 04 17:51:00 2017 -0400
@@ -0,0 +1,28 @@
+chr1	49721616	49821616
+chr1	95059425	95159425
+chr1	207236313	207336313
+chr2	73790843	73890843
+chr3	134465321	134565321
+chr4	43433669	43533669
+chr4	122032777	122132777
+chr5	12701747	12801747
+chr5	58501529	58601529
+chr5	152853250	152953250
+chr6	136085023	136185023
+chr6	147019529	147119529
+chr7	14192964	14292964
+chr7	125519883	125619883
+chr8	77652872	77752872
+chr8	108375665	108475665
+chr9	2984971	3084971
+chr10	978822	1078822
+chr11	18395046	18495046
+chr12	47273592	47373592
+chr12	60095778	60195778
+chr12	84854096	84954096
+chr12	95157539	95257539
+chr14	23982000	24082000
+chr16	1875335	1975335
+chr16	66789863	66889863
+chr18	64644131	64744131
+chr21	15966609	16066609

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/Feature1.bed	Fri Aug 04 17:51:00 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/Feature2.bed	Fri Aug 04 17:51:00 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/features.header.bed.txt	Fri Aug 04 17:51:00 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/test-data/input/regions.header.txt	Fri Aug 04 17:51:00 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 test-data/output_loadandplot/iwtomics.loadandplot.RData has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_loadandplot/iwtomics.loadandplot.features.txt	Fri Aug 04 17:51:00 2017 -0400
@@ -0,0 +1,1 @@
+ftr1	ftr2

Binary file test-data/output_loadandplot/iwtomics.loadandplot.pdf has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_loadandplot/iwtomics.loadandplot.regions.txt	Fri Aug 04 17:51:00 2017 -0400
@@ -0,0 +1,1 @@
+control	elem1	elem2	elem3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt	Fri Aug 04 17:51:00 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
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+Test: elem2 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt	Fri Aug 04 17:51:00 2017 -0400
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+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
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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
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+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
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+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
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+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
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+
+Test: elem2 vs control, on feature ftr2
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+
+Test: elem3 vs control, on feature ftr1
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+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
+Scale 42	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 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
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+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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_testandplot/iwtomics.testandplot.selectedfeatures.txt	Fri Aug 04 17:51:00 2017 -0400
@@ -0,0 +1,1 @@
+ftr1	ftr2

Binary file test-data/output_testandplot/iwtomics.testandplot.summaryplot.pdf has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_testandplot/iwtomics.testandplot.tests.txt	Fri Aug 04 17:51:00 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/testandplot.R	Fri Aug 04 17:51:00 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/testandplot.xml	Fri Aug 04 17:51:00 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>