# HG changeset patch
# User iuc
# Date 1501883460 14400
# Node ID 800c7e974e3bca91631912abf955829a09c394fc
planemo upload for repository https://github.com/fabio-cumbo/IWTomics4Galaxy commit 90c984bb9f803e1531fe4cb670e876809d48d205
diff -r 000000000000 -r 800c7e974e3b loadandplot.R
--- /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
diff -r 000000000000 -r 800c7e974e3b macros.xml
--- /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 @@
+
+ 1.0.0
+
+
+ bioconductor-iwtomics
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1080/10485252.2017.1306627
+
+ @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}
+ }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 800c7e974e3b plotwithscale.R
--- /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]]
+ and Plot
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+