# HG changeset patch
# User fabio
# Date 1496243190 14400
# Node ID 81faa1567178a2f4e13c3831392ab6c499385338
# Parent ed9594c25fad87450da195b83687880697ce8774
Deleted selected files
diff -r ed9594c25fad -r 81faa1567178 iwtomics/.Rapp.history
diff -r ed9594c25fad -r 81faa1567178 iwtomics/.Rhistory
--- a/iwtomics/.Rhistory Wed May 31 11:06:00 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-require(IWTomics)
-require(pheatmap)
-install.packages(pheatmap)
diff -r ed9594c25fad -r 81faa1567178 iwtomics/._.DS_Store
Binary file iwtomics/._.DS_Store has changed
diff -r ed9594c25fad -r 81faa1567178 iwtomics/._ETn_example
Binary file iwtomics/._ETn_example has changed
diff -r ed9594c25fad -r 81faa1567178 iwtomics/._example
Binary file iwtomics/._example has changed
diff -r ed9594c25fad -r 81faa1567178 iwtomics/._loadandplot.R
Binary file iwtomics/._loadandplot.R has changed
diff -r ed9594c25fad -r 81faa1567178 iwtomics/._plotwithscale.R
Binary file iwtomics/._plotwithscale.R has changed
diff -r ed9594c25fad -r 81faa1567178 iwtomics/._testandplot.R
Binary file iwtomics/._testandplot.R has changed
diff -r ed9594c25fad -r 81faa1567178 iwtomics/loadandplot.R
--- a/iwtomics/loadandplot.R Wed May 31 11:06:00 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,146 +0,0 @@
-if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
- require(tools,quietly = FALSE)
- args=commandArgs(TRUE)
-
- for (i in seq_along(args)) {
- message(args[[i]])
- }
-
- # 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$regionsfilenames,'\\|'))
- if(length(setdiff(regionsfilenames,row.names(regionsheader)))) {
- quit(save="no", status=11)
- stop('Not all regionsfilenames are present in the first column of regionsheader.')
- }
- id_regions=regionsheader[regionsfilenames,1]
- name_regions=regionsheader[regionsfilenames,2]
- }, error = function(err) {
- quit(save="no", status=10) #error on header file
- stop(err)
- })
- }else{
- eval(parse(text=args[[which(args_names=='regionsgalaxyids')]]))
- id_regions=paste0('data_',regionsgalaxyids)
- name_regions=paste0('data_',regionsgalaxyids)
- }
- featurespaths=unlist(strsplit(args_values$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)))) {
- quit(save="no", status=21)
- stop('Not all featuresfilenames are present in the first column of featuresheader.')
- }
- id_features=featuresheader[featuresfilenames,1]
- name_features=featuresheader[featuresfilenames,2]
- }, error = function(err) {
- quit(save="no", status=20) #error on header file
- stop(err)
- })
- }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$message)){
- quit(save="no", status=31) # error, not enough columns in input file
- }else if(grepl('duplicated regions',err$message)){
- quit(save="no", status=32) # error, duplicated regions in region file
- }else if(grepl('duplicated windows',err$message)){
- quit(save="no", status=33) # error, duplicated windows in feature file
- }else if(grepl('overlapping windows',err$message)){
- quit(save="no", status=34) # error, overlapping windows in feature file
- }else if(grepl('not all regions in datasets',err$message)){
- quit(save="no", status=35) # error, windows in feature files do not cover all regions in region files
- }else if(grepl('ifferent size windows',err$message)){
- quit(save="no", status=36) # error, all windows in a feature files must have the same size
- }
- #error loading data
-
- stop(err)
-
- 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) {
- quit(save="no", status=40) #error on smoothing
- stop(err)
- })
- }
-
- # 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{
- quit(save="no", status=255)
- stop("Missing IWTomics package")
-}
\ No newline at end of file
diff -r ed9594c25fad -r 81faa1567178 iwtomics/loadandplot.xml
--- a/iwtomics/loadandplot.xml Wed May 31 11:06:00 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,325 +0,0 @@
-
- Smooth and Plot
-
- macros.xml
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-& /dev/null
-]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-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) and Marzia A. Cremona (The Pennsylvania State University, USA).
-
-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
-
-
-
-
- @ARTICLE{
- iwt-functional-data,
- author = {Pini, Alessia and Vantini, Simone},
- title = {Interval-Wise Testing for functional data},
- journal = {Journal of Nonparametric Statistics},
- year = {2017},
- volume = {29},
- number = {2},
- pages = {407-424}
- }
-
-
- @MANUAL{
- iwtomics,
- author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
- title = {IWTomics: Interval-Wise Testing for Omics Data},
- note = {R package version 0.99.12},
- year = {2017}
- }
-
-
-
-
diff -r ed9594c25fad -r 81faa1567178 iwtomics/macros.xml
--- a/iwtomics/macros.xml Wed May 31 11:06:00 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-
- 1.0.0
-
-
- R
- bioconductor-iwtomics
-
-
-
\ No newline at end of file
diff -r ed9594c25fad -r 81faa1567178 iwtomics/plotwithscale.R
--- a/iwtomics/plotwithscale.R Wed May 31 11:06:00 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)$id_region2))){
- quit(save="no", status=10)
- stop('Wrong test ids')
- }
- if(sum(featureids!=idFeatures(regionsFeatures_test))){
- quit(save="no", status=20)
- stop('Wrong feature ids')
- }
- # retrieve test and features_subset ids
- id_features_subset=featureids[feature_subset]
- if(sum(duplicated(paste0(test_subset,id_features_subset)))){
- quit(save="no", status=30)
- stop('Two scale thresholds selected for the same test and feature.')
- }
- # If scale_subset=0, do not change the threshold
- default=(scale_subset==0)
- scale_subset=scale_subset[!default]
- test_subset=test_subset[!default]
- id_features_subset=id_features_subset[!default]
-
- # get scale threshold
- scale_threshold=lapply(regionsFeatures_test@test$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]]
- on Test Scale
-
- macros.xml
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-& /dev/null
-]]>
-
-
-
-
-
- ...
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-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
-
-
-
-
- @ARTICLE{
- iwt-functional-data,
- author = {A Pini and S. Vantini},
- title = {Interval-Wise Testing for functional data},
- journal = {Journal of Nonparametric Statistics},
- year = {2017},
- volume = {29},
- number = {2},
- pages = {407-424}
- }
-
-
- @MANUAL{
- iwtomics,
- author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
- title = {IWTomics: Interval-Wise Testing for Omics Data},
- note = {R package version 0.99.12},
- year = {2017}
- }
-
-
-
-
diff -r ed9594c25fad -r 81faa1567178 iwtomics/testandplot.R
--- a/iwtomics/testandplot.R Wed May 31 11:06:00 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){
- quit(save="no", status=10)
- stop('Wrong region ids')
- }
- if(length(setdiff(id_features_subset,idFeatures(regionsFeatures)))!=0){
- quit(save="no", status=20)
- stop('Wrong feature ids')
- }
- if(sum(duplicated(paste0(id_region1,id_region2)))){
- quit(save="no", status=30)
- stop('Same test repeated multiple times.')
- }
-
- # 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) {
- quit(save="no", status=40) #error testing
- stop(err)
- })
-
- # 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{
- quit(save="no", status=255)
- stop("Missing IWTomics package")
-}
\ No newline at end of file
diff -r ed9594c25fad -r 81faa1567178 iwtomics/testandplot.xml
--- a/iwtomics/testandplot.xml Wed May 31 11:06:00 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,239 +0,0 @@
-
- and Plot
-
- macros.xml
-
-
-
-
-
-
-
-
-
-
-
-
-& /dev/null
-]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-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
-
-
-
-
- @ARTICLE{
- iwt-functional-data,
- author = {A Pini and S. Vantini},
- title = {Interval-Wise Testing for functional data},
- journal = {Journal of Nonparametric Statistics},
- year = {2017},
- volume = {29},
- number = {2},
- pages = {407-424}
- }
-
-
- @MANUAL{
- iwtomics,
- author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
- title = {IWTomics: Interval-Wise Testing for Omics Data},
- note = {R package version 0.99.12},
- year = {2017}
- }
-
-
-
-