Mercurial > repos > pavlo-lutsik > rnbeads
changeset 32:528511446522 draft
Deleted selected files
| author | pavlo-lutsik |
|---|---|
| date | Fri, 05 Jul 2013 08:17:44 -0400 |
| parents | aad84663f9c2 |
| children | 4feb5eba202c |
| files | RnBeadsGalaxy.R faq.section.doc galaxy.on.the.cloud galaxy_faq.docx install.rnbeads.R rnb.cloud.4.07.analysis.log rnbeads.xml rnbeads_galaxy_wrapper.sh rnbeads_repos.txt.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 11 files changed, 0 insertions(+), 1024 deletions(-) [+] |
line wrap: on
line diff
--- a/RnBeadsGalaxy.R Fri Jul 05 08:03:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,198 +0,0 @@ -#msg.file<-file("RnBeads.messages.out", open="w") -#sink(file=msg.file) - -suppressWarnings(suppressPackageStartupMessages(library(RnBeads))) -suppressWarnings(suppressPackageStartupMessages(library(getopt))) - -#all.opts<-names(rnb.options()) -opt.class<-RnBeads:::OPTION.TYPES[-28] -all.opts<-names(opt.class) -#all.opts<-paste("--", all.opts, sep="") -#all.opts<-gsub("\\.([a-z])", "\\U\\1", all.opts, perl=TRUE) -all.opts<-gsub("\\.","-", all.opts) -#opt.class<-sapply(rnb.options(), class) - -rnb.opt.spec<-data.frame( - Long=all.opts, - Short=as.character(1:length(all.opts)), - Mask=c(1,2)[as.integer((opt.class=="logical"))+1], - Type=opt.class) - -### automated xml file preparation -xml.strings<-apply(rnb.opt.spec,1, function(row){ - - opt.lab<-gsub("-", ".", row[1]) - opt.def.val<-rnb.getOption(opt.lab) - opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE) - tf.opt<-"\t\t\t<option value=\"True\">True</option>\n\t\t\t<option value=\"False\">False</option>" - opt.lab<-paste(opt.lab, gsub("\\."," ", row[4]), sep=", ") - if(row[4]=="logical"){ - opt.type<-'select' - if(!is.null(opt.def.val) && opt.def.val) - opt.def.val<-"1" else - opt.def.val<-"0" - string<-sprintf("\t\t<param name=\"%s\" type=\"%s\" label=\"%s\" value=\"%s\">\n%s\n\t\t</param>\n", opt.name, opt.type, opt.lab, opt.def.val, tf.opt) - }else{ - opt.type<-'text' - if(!is.null(opt.def.val) && opt.def.val!="") - opt.def.val<-paste(opt.def.val, collapse=",") else - opt.def.val<-"" - string<-sprintf("\t\t<param name=\"%s\" type=\"%s\" label=\"%s\" value=\"%s\"/>\n", opt.name, opt.type, opt.lab, opt.def.val) - } - string - }) - -cat(xml.strings, sep="", file="automated.settings.xml.txt") - -opt.def.strings<-apply(rnb.opt.spec,1, function(row){ - - opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE) - opt.long<-row[1] - opt.short<-row[2] - - if(row[4]=="logical"){ - def.string<-sprintf("#if str( $options.%s ) == \"True\"\n\t--%s\n#end if\n", opt.name, opt.long) - }else{ - def.string<-sprintf("#if str( $options.%s ) != \"\"\n\t--%s=\"$options.%s\" \n#end if\n", opt.name, opt.long, opt.name) - } - def.string - - }) -cat(opt.def.strings, sep="", file="automated.option.assignments.txt") - - -rnb.opt.spec$Type<-gsub("\\.vector", "", rnb.opt.spec$Type) -rnb.opt.spec$Type<-gsub("numeric", "double", rnb.opt.spec$Type) -rnb.opt.spec<-rbind(data.frame( - Long=c("data-type", "pheno", "idat-dir","idat-files","bed-files", "gs-report", "geo-series", "betas", "pvals","output-file", "report-dir"), - Short=c("d","s","a","i","f","g","e","b","p","r","o"), - Mask=c(1,2,2,2,2,2,2,2,2,1,1), - Type=c("character","character","character","character","character","character","character","character","character","character", "character")), - rnb.opt.spec) - -opts<-getopt(as.matrix(rnb.opt.spec)) -#opts<-getopt(as.matrix(rnb.opt.spec), opt=list("--data-type=idats","--report-dir=dir", "--idats=file1\tfile2")) -print(opts) - -if(opts[["data-type"]]=="idatDir"){ - - data.source<-list() - data.type<-"idat.dir" - data.source[["idat.dir"]]<-opts[["idat-dir"]] - data.source[["sample.sheet"]]<-opts[["pheno"]] - -}else if(opts[["data-type"]]=="idatFiles"){ - - data.type<-"idat.dir" - file.string<-gsub(" ","", opts[["idat-files"]]) - files<-strsplit(file.string, ",")[[1]] - files<-files[files!=""] - bed.dir<-sprintf("%s_beds",opts[["report-dir"]]) - dir.create(bed.dir) - file.copy(files, bed.dir) - for(dat.file in list.files(bed.dir, full.names = TRUE)){ - file.rename(dat.file, gsub("\\.dat", ".bed", dat.file)) - } - data.source<-list() - data.source[["bed.dir"]]<-bed.dir - data.source[["sample.sheet"]]<-opts[["pheno"]] - - -}else if(opts[["data-type"]]=="GS.report"){ - - data.type<-"GS.report" - data.source<-opts[["gs-report"]] - -}else if(opts[["data-type"]]=="GEO"){ - - data.type<-"GEO" - data.source<-opts[["geo-series"]] - -}else if(opts[["data-type"]]=="data.files"){ - - data.type<-"GEO" - data.source<-opts[["geo-series"]] - -}else if(opts[["data-type"]]=="data.files"){ - - data.type<-"data.files" - data.source<-c(opts[["pheno"]], opts[["betas"]]) - if(!is.null(opts[["pvals"]])) - data.source<-c(data.source, opts[["pvals"]]) - -}else if(opts[["data-type"]]=="bed.dir"){ - - data.type<-"bed.dir" - file.string<-gsub(" ","", opts[["bed-files"]]) - files<-strsplit(file.string, ",")[[1]] - files<-files[files!=""] - bed.dir<-sprintf("%s_beds",opts[["report-dir"]]) - dir.create(bed.dir) - file.copy(files, bed.dir) - for(dat.file in list.files(bed.dir, full.names = TRUE)){ - file.rename(dat.file, gsub("\\.dat", ".bed", dat.file)) - } - data.source<-list() - data.source[["bed.dir"]]<-bed.dir - - logger.start(fname="NA") - sample.sheet<-rnb.read.annotation(opts[["pheno"]]) - logger.close() - if(length(files) < nrow(sample.sheet)) - stop("Not all bed files are present") - - cn<-colnames(sample.sheet) - dat.files<-sapply(strsplit(files, "\\/"), function(el) el[length(el)]) - sample.sheet<-cbind(sample.sheet, gsub("\\.dat", ".bed", dat.files)) - colnames(sample.sheet)<-c(cn, "BED_files") - data.source[["sample.sheet"]]<-sample.sheet -} - -if("logging" %in% names(opts)){ # TODO create a cleaner way of checking whether the full options set was supplied - - dump<-sapply(names(opt.class), function(on){ - getoptname<-gsub("-", "\\.","-",on) - if(getoptname %in% names(opts)){ - if(opt.class[on]=="logical"){ - ov<-TRUE - }else if(opt.class %in% c("character","character.vector")){ - ov<-opts[[getoptname]] - ov<-gsub("\"", "", ov) - if(opt.class=="character.vector"){ - ov<-as.character(strsplit(ov,",")) - } - - }else if(opt.class %in% c("integer","numeric","integer.vector","numeric.vector")){ - ov<-opts[[getoptname]] - ov<-gsub("\"", "", ov) - if(opt.class %in% c("integer.vector","numeric.vector")){ - ov<-as.character(strsplit(ov,",")) - } - } - eval(parse(text=sprintf("rnb.options(%s=ov)",on))) - } - }) - - logical.opts<-names(opt.class[opt.class=="logical"]) - logical.opts.false<-logical.opts[!logical.opts %in% gsub("-",".",names(opts))] - - - dump<-sapply(logical.opts.false, function(on){ - eval(parse(text=sprintf("rnb.options(%s=FALSE)",on))) - }) -} - -print(rnb.options()) - -#report.out.dir<-sprintf("%s_rnbReport", tempdir()) -report.out.dir<-opts[["report-dir"]] -print("Starting RnBeads with the following inputs:") -print(data.source) -print(report.out.dir) -print(data.type) -rnb.run.analysis(data.source=data.source, dir.report=report.out.dir, data.type=data.type) - - -#sink(file=NULL) -#flush(msg.file) -#close(msg.file) \ No newline at end of file
--- a/install.rnbeads.R Fri Jul 05 08:03:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -source("http://rnbeads.mpi-inf.mpg.de/install.R") \ No newline at end of file
--- a/rnb.cloud.4.07.analysis.log Fri Jul 05 08:03:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,265 +0,0 @@ -2013-07-04 12:48:18 STATUS STARTED RnBeads Pipeline -2013-07-04 12:48:18 INFO Initialized report index and saved to index.html -2013-07-04 12:48:18 STATUS STARTED Loading Data -2013-07-04 12:48:18 STATUS STARTED Loading GEO Data Series -2013-07-04 12:53:38 INFO Loaded 1 data series from GSE38268 -2013-07-04 12:53:38 INFO Extracted 6 samples from series 1 -2013-07-04 12:53:38 INFO Parsed characteristics_ch1 sample information -2013-07-04 12:53:38 STATUS COMPLETED Loading GEO Data Series -2013-07-04 12:54:49 STATUS Loaded data from GSE38268. Output object is of class RnBeadSet -2013-07-04 12:54:50 STATUS Added data loading section -2013-07-04 12:54:50 STATUS COMPLETED Loading Data -2013-07-04 12:54:50 STATUS STARTED Normalization -2013-07-04 12:54:50 WARNING Incompatible values for object and method. Changed the normalization method to "none" -2013-07-04 12:54:50 WARNING Incompatible values for object and background correction flag. Disabled the background correction -2013-07-04 12:54:50 STATUS Performed normalization with method "swan" -2013-07-04 12:54:53 STATUS Added normalization section -2013-07-04 12:54:53 STATUS COMPLETED Normalization -2013-07-04 12:54:54 INFO Initialized report index and saved to index.html -2013-07-04 12:54:54 STATUS STARTED Quality Control -2013-07-04 12:54:54 STATUS STARTED Quality Control Section -2013-07-04 12:54:54 INFO No quality information present in the dataset -2013-07-04 12:54:54 STATUS COMPLETED Quality Control Section -2013-07-04 12:54:54 STATUS COMPLETED Quality Control -2013-07-04 12:54:54 STATUS STARTED Visualizing Sample Mixups -2013-07-04 12:54:54 STATUS STARTED Mixups Visualization Section -2013-07-04 12:55:15 STATUS Added SNP heatmap -2013-07-04 12:55:15 STATUS COMPLETED Mixups Visualization Section -2013-07-04 12:55:15 STATUS COMPLETED Visualizing Sample Mixups -2013-07-04 12:55:15 INFO Initialized report index and saved to index.html -2013-07-04 12:55:15 STATUS STARTED Filtering -2013-07-04 12:55:23 STATUS STARTED Probe Context Removal -2013-07-04 12:56:00 STATUS Removed 3156 probe(s) out of context -2013-07-04 12:56:01 STATUS Saved removed sites to /mnt/galaxy/files/000/dataset_3_files/filtering_data/removed_sites_context.csv -2013-07-04 12:56:01 STATUS Added a corresponding section to the report -2013-07-04 12:56:01 STATUS COMPLETED Probe Context Removal -2013-07-04 12:56:03 STATUS STARTED Removal of SNP-enriched Sites -2013-07-04 12:56:38 STATUS Removed 18987 sites that overlap sites with more than 2 SNP(s) -2013-07-04 12:56:38 STATUS Saved removed sites to /mnt/galaxy/files/000/dataset_3_files/filtering_data/removed_sites_snp.csv -2013-07-04 12:56:38 STATUS Added a corresponding section to the report -2013-07-04 12:56:38 STATUS COMPLETED Removal of SNP-enriched Sites -2013-07-04 12:56:39 INFO Omitting Greedycut because detection p-values are missing -2013-07-04 12:56:42 STATUS STARTED Summary of Filtering Procedures -2013-07-04 12:56:46 STATUS Added summary table of removed and retained values -2013-07-04 12:57:47 STATUS Added comparison between removed and retained beta values -2013-07-04 12:57:47 STATUS COMPLETED Summary of Filtering Procedures -2013-07-04 12:57:47 STATUS COMPLETED Filtering -2013-07-04 12:57:47 INFO Initialized report index and saved to index.html -2013-07-04 12:57:47 STATUS STARTED Dimension Reduction Techniques -2013-07-04 12:57:48 WARNING Removed 4301 loci ( sites ) because they contain missing values -2013-07-04 12:57:49 STATUS Calculated PCA coordinates -2013-07-04 12:57:49 STATUS Calculated MDS coordinates using manhattan distance -2013-07-04 12:57:49 STATUS Calculated MDS coordinates using euclidean distance -2013-07-04 12:57:50 WARNING Removed 491 loci ( tiling ) because they contain missing values -2013-07-04 12:57:50 STATUS Calculated PCA coordinates -2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance -2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance -2013-07-04 12:57:50 WARNING Removed 25 loci ( genes ) because they contain missing values -2013-07-04 12:57:50 STATUS Calculated PCA coordinates -2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance -2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance -2013-07-04 12:57:50 WARNING Removed 30 loci ( promoters ) because they contain missing values -2013-07-04 12:57:50 STATUS Calculated PCA coordinates -2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance -2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance -2013-07-04 12:57:51 WARNING Removed 15 loci ( cpgislands ) because they contain missing values -2013-07-04 12:57:51 STATUS Calculated PCA coordinates -2013-07-04 12:57:51 STATUS Calculated MDS coordinates using manhattan distance -2013-07-04 12:57:51 STATUS Calculated MDS coordinates using euclidean distance -2013-07-04 12:57:51 INFO Mapping 2 traits to point colors and types -2013-07-04 13:14:59 INFO Principal components that explain at least 95 % of the total variance: 5 -2013-07-04 13:14:59 INFO Saved percentage of total variance to pca_variance_explained_1.csv -2013-07-04 13:15:03 INFO Principal components that explain at least 95 % of the total variance: 5 -2013-07-04 13:15:03 INFO Saved percentage of total variance to pca_variance_explained_2.csv -2013-07-04 13:15:08 INFO Principal components that explain at least 95 % of the total variance: 5 -2013-07-04 13:15:08 INFO Saved percentage of total variance to pca_variance_explained_3.csv -2013-07-04 13:15:12 INFO Principal components that explain at least 95 % of the total variance: 5 -2013-07-04 13:15:12 INFO Saved percentage of total variance to pca_variance_explained_4.csv -2013-07-04 13:15:16 INFO Principal components that explain at least 95 % of the total variance: 5 -2013-07-04 13:15:16 INFO Saved percentage of total variance to pca_variance_explained_5.csv -2013-07-04 13:15:20 STATUS Created scatter plots and CDFs summarizing the reduced dimensional representations -2013-07-04 13:15:20 STATUS COMPLETED Dimension Reduction Techniques -2013-07-04 13:15:20 STATUS STARTED Tests for Associations -2013-07-04 13:15:20 INFO Testing the following traits for associations: tumour site; tissue -2013-07-04 13:15:20 STATUS Computed correlations between principal components and traits. -2013-07-04 13:15:20 STATUS Computed pairwise correlations between traits. -2013-07-04 13:15:20 STATUS COMPLETED Tests for Associations -2013-07-04 13:15:48 STATUS STARTED Quality-associated Batch Effects -2013-07-04 13:15:48 WARNING No quality information available -2013-07-04 13:15:48 STATUS COMPLETED Quality-associated Batch Effects -2013-07-04 13:15:48 INFO Initialized report index and saved to index.html -2013-07-04 13:15:49 STATUS STARTED Methylation Profiles -2013-07-04 13:15:49 INFO Designed color mappings for probe type and CGI status -2013-07-04 13:15:57 STATUS STARTED Methylation Value Distributions - Sample Groups -2013-07-04 13:19:31 STATUS COMPLETED Methylation Value Distributions - Sample Groups -2013-07-04 13:19:31 STATUS STARTED Methylation Value Distributions - Probe Categories -2013-07-04 13:22:46 STATUS COMPLETED Methylation Value Distributions - Probe Categories -2013-07-04 13:22:47 STATUS STARTED Scatter Plots of Mean Beta vs Variance -2013-07-04 13:22:47 INFO Sample subgroups are defined by: tumour site; tissue -2013-07-04 13:22:48 WARNING Removed 10 loci with missing values in group all samples -2013-07-04 13:31:43 WARNING Removed 1448 loci with missing values in group base of tongue (based on tumour site) -2013-07-04 13:40:36 WARNING Removed 26 loci with missing values in group tonsil (based on tumour site) -2013-07-04 13:49:33 WARNING Removed 56 loci with missing values in group HPV+ HNSCC tumor (based on tissue) -2013-07-04 13:58:28 WARNING Removed 78 loci with missing values in group HPV- HNSCC tumor (based on tissue) -2013-07-04 14:07:20 STATUS Created 20 scatter plots of methylation variance on the site level -2013-07-04 14:07:21 WARNING Removed 1 loci with missing values in group all samples -2013-07-04 14:08:44 WARNING Removed 159 loci with missing values in group base of tongue (based on tumour site) -2013-07-04 14:10:05 WARNING Removed 2 loci with missing values in group tonsil (based on tumour site) -2013-07-04 14:11:26 WARNING Removed 4 loci with missing values in group HPV+ HNSCC tumor (based on tissue) -2013-07-04 14:12:48 WARNING Removed 7 loci with missing values in group HPV- HNSCC tumor (based on tissue) -2013-07-04 14:14:34 WARNING Removed 9 loci with missing values in group base of tongue (based on tumour site) -2013-07-04 14:16:42 WARNING Removed 8 loci with missing values in group base of tongue (based on tumour site) -2013-07-04 14:17:34 WARNING Removed 1 loci with missing values in group HPV+ HNSCC tumor (based on tissue) -2013-07-04 14:18:49 WARNING Removed 2 loci with missing values in group base of tongue (based on tumour site) -2013-07-04 14:20:26 STATUS Created 40 scatter plots of methylation variance on the region level -2013-07-04 14:20:26 STATUS COMPLETED Scatter Plots of Mean Beta vs Variance -2013-07-04 14:20:26 STATUS STARTED Deviation Plots -2013-07-04 14:49:08 STATUS Created 15 deviation plots on the site level -2013-07-04 15:04:01 STATUS Created 20 deviation plots on the region level -2013-07-04 15:04:02 STATUS Added summary table of variabilities -2013-07-04 15:04:02 STATUS COMPLETED Deviation Plots -2013-07-04 15:04:02 STATUS STARTED Sample Clustering -2013-07-04 15:04:02 STATUS STARTED Agglomerative Hierarchical Clustering -2013-07-04 15:04:02 STATUS Performed clustering on sites using correlation as a distance metric -2013-07-04 15:04:02 STATUS Performed clustering on sites using manhattan as a distance metric -2013-07-04 15:04:03 STATUS Performed clustering on sites using euclidean as a distance metric -2013-07-04 15:04:03 STATUS Performed clustering on tiling using correlation as a distance metric -2013-07-04 15:04:03 STATUS Performed clustering on tiling using manhattan as a distance metric -2013-07-04 15:04:03 STATUS Performed clustering on tiling using euclidean as a distance metric -2013-07-04 15:04:03 STATUS Completed clustering for tiling -2013-07-04 15:04:03 STATUS Performed clustering on genes using correlation as a distance metric -2013-07-04 15:04:03 STATUS Performed clustering on genes using manhattan as a distance metric -2013-07-04 15:04:03 STATUS Performed clustering on genes using euclidean as a distance metric -2013-07-04 15:04:03 STATUS Completed clustering for genes -2013-07-04 15:04:03 STATUS Performed clustering on promoters using correlation as a distance metric -2013-07-04 15:04:03 STATUS Performed clustering on promoters using manhattan as a distance metric -2013-07-04 15:04:03 STATUS Performed clustering on promoters using euclidean as a distance metric -2013-07-04 15:04:03 STATUS Completed clustering for promoters -2013-07-04 15:04:03 STATUS Performed clustering on cpgislands using correlation as a distance metric -2013-07-04 15:04:03 STATUS Performed clustering on cpgislands using manhattan as a distance metric -2013-07-04 15:04:04 STATUS Performed clustering on cpgislands using euclidean as a distance metric -2013-07-04 15:04:04 STATUS Completed clustering for cpgislands -2013-07-04 15:04:04 STATUS COMPLETED Agglomerative Hierarchical Clustering -2013-07-04 15:04:04 STATUS STARTED Clustering Section -2013-07-04 15:04:05 STATUS STARTED Generating Heatmaps -2013-07-04 15:04:05 STATUS STARTED Region type: sites -2013-07-04 15:12:40 STATUS COMPLETED Region type: sites -2013-07-04 15:12:40 STATUS STARTED Region type: tiling -2013-07-04 15:21:19 STATUS COMPLETED Region type: tiling -2013-07-04 15:21:19 STATUS STARTED Region type: genes -2013-07-04 15:29:56 STATUS COMPLETED Region type: genes -2013-07-04 15:29:56 STATUS STARTED Region type: promoters -2013-07-04 15:38:33 STATUS COMPLETED Region type: promoters -2013-07-04 15:38:33 STATUS STARTED Region type: cpgislands -2013-07-04 15:47:09 STATUS COMPLETED Region type: cpgislands -2013-07-04 15:47:10 STATUS Created 360 heatmaps based on the clustering results -2013-07-04 15:47:10 STATUS COMPLETED Generating Heatmaps -2013-07-04 15:47:10 STATUS STARTED Adding Color Legends -2013-07-04 15:50:15 STATUS COMPLETED Adding Color Legends -2013-07-04 15:50:15 STATUS STARTED Estimating Optimal Numbers of Clusters -2013-07-04 15:51:21 STATUS Estimated number of clusters based on mean silhouette value -2013-07-04 15:51:21 STATUS COMPLETED Estimating Optimal Numbers of Clusters -2013-07-04 15:51:21 STATUS STARTED Overlapping Clusters with Sample Traits -2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_1.csv -2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_2.csv -2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_3.csv -2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_4.csv -2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_5.csv -2013-07-04 15:52:26 STATUS COMPLETED Overlapping Clusters with Sample Traits -2013-07-04 15:52:26 STATUS COMPLETED Clustering Section -2013-07-04 15:52:26 STATUS COMPLETED Sample Clustering -2013-07-04 15:52:26 STATUS STARTED Regional Methylation Profiling -2013-07-04 15:52:26 STATUS STARTED Computing Regional Profiles Based on Binning -2013-07-04 15:52:26 STATUS STARTED Processing Region Type: genes -2013-07-04 16:03:01 STATUS Set region annotation and site membership -2013-07-04 16:04:02 STATUS Computed binned methylation values -2013-07-04 16:04:02 STATUS COMPLETED Processing Region Type: genes -2013-07-04 16:04:02 STATUS STARTED Processing Region Type: promoters -2013-07-04 16:14:38 STATUS Set region annotation and site membership -2013-07-04 16:15:29 STATUS Computed binned methylation values -2013-07-04 16:15:29 STATUS COMPLETED Processing Region Type: promoters -2013-07-04 16:15:29 STATUS STARTED Processing Region Type: cpgislands -2013-07-04 16:25:46 STATUS Set region annotation and site membership -2013-07-04 16:26:38 STATUS Computed binned methylation values -2013-07-04 16:26:38 STATUS COMPLETED Processing Region Type: cpgislands -2013-07-04 16:26:38 STATUS COMPLETED Computing Regional Profiles Based on Binning -2013-07-04 16:26:38 STATUS STARTED Creating a Corresponding Section in the Report -2013-07-04 16:26:38 STATUS Plotting region profiles for region genes and column tumour site ... -2013-07-04 16:28:31 STATUS Plotting region profiles for region genes and column tissue ... -2013-07-04 16:29:44 STATUS Plotting region profiles for region promoters and column tumour site ... -2013-07-04 16:30:31 STATUS Plotting region profiles for region promoters and column tissue ... -2013-07-04 16:31:15 STATUS Plotting region profiles for region cpgislands and column tumour site ... -2013-07-04 16:32:16 STATUS Plotting region profiles for region cpgislands and column tissue ... -2013-07-04 16:33:13 STATUS COMPLETED Creating a Corresponding Section in the Report -2013-07-04 16:33:13 STATUS COMPLETED Regional Methylation Profiling -2013-07-04 16:33:13 STATUS COMPLETED Methylation Profiles -2013-07-04 16:33:13 INFO Initialized report index and saved to index.html -2013-07-04 16:33:14 STATUS STARTED Differential Methylation - Analysis -2013-07-04 16:33:14 INFO Using 0 permutation tests -2013-07-04 16:33:14 INFO Using columns: title,geo_accession,status,submission_date,last_update_date,type,channel_count,source_name_ch1,organism_ch1,molecule_ch1,extract_protocol_ch1,label_ch1,label_protocol_ch1,taxid_ch1,hyb_protocol,scan_protocol,description,data_processing,platform_id,contact_name,contact_email,contact_laboratory,contact_department,contact_institute,contact_address,contact_city,contact_zip/postal_code,contact_country,supplementary_file,data_row_count,tumour site,tissue -2013-07-04 16:33:14 INFO Using region types: tiling,genes,promoters,cpgislands -2013-07-04 16:33:14 STATUS STARTED Comparison Information: tumour site -2013-07-04 16:33:14 STATUS STARTED Comparing base of tongue-tonsil -2013-07-04 16:33:14 STATUS STARTED Computing Differential Methylation Table (Site Level) -2013-07-04 16:33:21 INFO Some t-test p-values are NA. They are treated as 1 in FDR adjustment -2013-07-04 16:33:28 STATUS COMPLETED Computing Differential Methylation Table (Site Level) -2013-07-04 16:33:28 STATUS STARTED Computing Differential Methylation Tables (Region Level) -2013-07-04 16:45:21 INFO Some p-values are NA. They are treated as 1 in FDR adjustment -2013-07-04 16:45:21 STATUS Computed table for tiling -2013-07-04 16:48:07 INFO Some p-values are NA. They are treated as 1 in FDR adjustment -2013-07-04 16:48:07 STATUS Computed table for genes -2013-07-04 16:50:48 INFO Some p-values are NA. They are treated as 1 in FDR adjustment -2013-07-04 16:50:48 STATUS Computed table for promoters -2013-07-04 16:53:07 INFO Some p-values are NA. They are treated as 1 in FDR adjustment -2013-07-04 16:53:07 STATUS Computed table for cpgislands -2013-07-04 16:53:07 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) -2013-07-04 16:53:07 STATUS COMPLETED Comparing base of tongue-tonsil -2013-07-04 16:53:07 STATUS COMPLETED Comparison Information: tumour site -2013-07-04 16:53:07 STATUS STARTED Comparison Information: tissue -2013-07-04 16:53:07 STATUS STARTED Comparing HPV+ HNSCC tumor-HPV- HNSCC tumor -2013-07-04 16:53:07 STATUS STARTED Computing Differential Methylation Table (Site Level) -2013-07-04 16:53:12 INFO Some t-test p-values are NA. They are treated as 1 in FDR adjustment -2013-07-04 16:53:17 STATUS COMPLETED Computing Differential Methylation Table (Site Level) -2013-07-04 16:53:17 STATUS STARTED Computing Differential Methylation Tables (Region Level) -2013-07-04 17:04:12 INFO Some p-values are NA. They are treated as 1 in FDR adjustment -2013-07-04 17:04:13 STATUS Computed table for tiling -2013-07-04 17:06:56 STATUS Computed table for genes -2013-07-04 17:09:29 INFO Some p-values are NA. They are treated as 1 in FDR adjustment -2013-07-04 17:09:29 STATUS Computed table for promoters -2013-07-04 17:11:43 STATUS Computed table for cpgislands -2013-07-04 17:11:43 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) -2013-07-04 17:11:43 STATUS COMPLETED Comparing HPV+ HNSCC tumor-HPV- HNSCC tumor -2013-07-04 17:11:43 STATUS COMPLETED Comparison Information: tissue -2013-07-04 17:11:43 INFO Skipping enrichment analysis of differentially methylated regions -2013-07-04 17:11:43 STATUS COMPLETED Differential Methylation - Analysis -2013-07-04 17:11:43 STATUS STARTED Differential Methylation - Report Generation -2013-07-04 17:11:43 STATUS Added introductory section -2013-07-04 17:11:43 STATUS STARTED Adding Site Level Information -2013-07-04 18:03:20 STATUS COMPLETED Adding Site Level Information -2013-07-04 18:03:20 STATUS STARTED Adding Region Level Information -2013-07-04 18:31:24 STATUS COMPLETED Adding Region Level Information -2013-07-04 18:31:24 STATUS COMPLETED Differential Methylation - Report Generation -2013-07-04 18:31:25 INFO Initialized report index and saved to index.html -2013-07-04 18:31:25 STATUS STARTED Data Export -2013-07-04 18:31:25 STATUS STARTED Exporting RnBSet -2013-07-04 18:31:25 STATUS STARTED Exporting sites -2013-07-04 18:31:25 STATUS STARTED Creating UCSC Track Hub -- bigBed -2013-07-04 18:31:25 STATUS STARTED Conversion to BED -2013-07-04 18:33:46 STATUS COMPLETED Conversion to BED -2013-07-04 18:33:46 STATUS STARTED Creating UCSC Track Hub -2013-07-04 18:34:06 STATUS COMPLETED Creating UCSC Track Hub -2013-07-04 18:34:06 STATUS COMPLETED Creating UCSC Track Hub -- bigBed -2013-07-04 18:34:06 STATUS STARTED Creating UCSC Track Hub -- bigWig -2013-07-04 18:34:06 STATUS STARTED Conversion to bedGraph -2013-07-04 18:36:10 STATUS COMPLETED Conversion to bedGraph -2013-07-04 18:36:10 STATUS STARTED Creating UCSC Track Hub -2013-07-04 18:36:28 STATUS COMPLETED Creating UCSC Track Hub -2013-07-04 18:36:28 STATUS COMPLETED Creating UCSC Track Hub -- bigWig -2013-07-04 18:36:28 STATUS COMPLETED Exporting sites -2013-07-04 18:36:28 STATUS COMPLETED Exporting RnBSet -2013-07-04 18:36:28 STATUS STARTED Writing export report -2013-07-04 18:36:28 STATUS COMPLETED Writing export report -2013-07-04 18:36:28 STATUS COMPLETED Data Export -2013-07-04 18:36:28 INFO Initialized report index and saved to index.html -2013-07-04 18:36:29 STATUS COMPLETED RnBeads Pipeline -
--- a/rnbeads.xml Fri Jul 05 08:03:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,506 +0,0 @@ -<?xml version="0.9"?> -<tool id="rnbeads" name="RnBeads" version="0.9"> - <description>Performs RnBeads analysis for the selected set of </description> - <requirements> - <requirement type="set_environment" version="1.0">R_SCRIPTS_PATH</requirement> - <requirement type="package" version="3.0.0">R</requirement> - </requirements> - <command interpreter="bash">rnbeads_galaxy_wrapper.sh - --report-dir="$html_file.extra_files_path" - --output-file="$html_file" - #if str( $inputDataSelector.dataType ) == "idats" - --pheno="$inputDataSelector.sampleAnnotations" - #end if - #if str( $inputDataSelector.dataType ) != "idats" - #pass - #else if str( $inputDataSelector.idatSelector.idatSource ) == "history" - --data-type="idatFiles" - #set $idatList="" - #for $input_file in $inputDataSelector.idatSelector.idatSeries: - #set $idatList+=str( $input_file.idatFile ) - #set $idatList+="," - #end for - --idat-files="$idatList" - #else: - --data-type="idatDir" - --idat-dir="$inputDataSelector.idatSelector.idatRepo.fields.path" - #end if - #if str( $inputDataSelector.dataType ) == "gsreport" - --data-type="GS.report" - --gs-report="$inputDataSelector.gsReportFile" - #end if - #if str( $inputDataSelector.dataType ) == "geo" - --data-type="GEO" - --geo-series=$inputDataSelector.geoSeries - #end if - #if str( $inputDataSelector.dataType ) == "tables" - --data-type="data.files" - --pheno="$inputDataSelector.sampleAnnotations" - #end if - #if str( $inputDataSelector.dataType ) == "tables" - --data-type="data.files" - --pheno="$inputDataSelector.sampleAnnotations" - --betas="$inputDataSelector.betaTable" - --pvals="$inputDataSelector.pvalTable" - #end if - #if str( $inputDataSelector.dataType ) == "bed" - --data-type="bed.dir" - --pheno="$inputDataSelector.sampleAnnotations" - #set $bedList="" - #for $input_file in $inputDataSelector.bedSeries: - #set $bedList+=str( $input_file.bedFile ) - #set $bedList+="," - #end for - --bed-files="$bedList" - #end if - #if str( $options.optionSet ) == "full" - #if str( $options.analysisName ) != "" - --analysis-name="$options.analysisName" - #end if - #if str( $options.logging ) == "True" - --logging - #end if - #if str( $options.email ) != "" - --email="$options.email" - #end if - #if str( $options.assembly ) != "" - --assembly="$options.assembly" - #end if - #if str( $options.columnsPairing ) != "" - --columns-pairing="$options.columnsPairing" - #end if - #if str( $options.analyzeSites ) == "True" - --analyze-sites - #end if - #if str( $options.regionTypes ) != "" - --region-types="$options.regionTypes" - #end if - #if str( $options.identifiersColumn ) != "" - --identifiers-column="$options.identifiersColumn" - #end if - #if str( $options.pointsCategory ) != "" - --points-category="$options.pointsCategory" - #end if - #if str( $options.colorsCategory ) != "" - --colors-category="$options.colorsCategory" - #end if - #if str( $options.colorsGradient ) != "" - --colors-gradient="$options.colorsGradient" - #end if - #if str( $options.minGroupSize ) != "" - --min-group-size="$options.minGroupSize" - #end if - #if str( $options.maxGroupCount ) != "" - --max-group-count="$options.maxGroupCount" - #end if - #if str( $options.gzLargeFiles ) == "True" - --gz-large-files - #end if - #if str( $options.strandSpecific ) == "True" - --strand-specific - #end if - #if str( $options.replicateIdColumn ) != "" - --replicate-id-column="$options.replicateIdColumn" - #end if - #if str( $options.loadingNormalization ) == "True" - --loading-normalization - #end if - #if str( $options.loadingDefaultDataType ) != "" - --loading-default-data-type="$options.loadingDefaultDataType" - #end if - #if str( $options.loadingTableSeparator ) != "" - --loading-table-separator="$options.loadingTableSeparator" - #end if - #if str( $options.loadingBedStyle ) != "" - --loading-bed-style="$options.loadingBedStyle" - #end if - #if str( $options.loadingBedColumns ) != "" - --loading-bed-columns="$options.loadingBedColumns" - #end if - #if str( $options.loadingBedFrameShift ) != "" - --loading-bed-frame-shift="$options.loadingBedFrameShift" - #end if - #if str( $options.normalizationMethod ) != "" - --normalization-method="$options.normalizationMethod" - #end if - #if str( $options.normalizationBackgroundMethod ) != "" - --normalization-background-method="$options.normalizationBackgroundMethod" - #end if - #if str( $options.qc ) == "True" - --qc - #end if - #if str( $options.qcBoxplots ) == "True" - --qc-boxplots - #end if - #if str( $options.qcBarplots ) == "True" - --qc-barplots - #end if - #if str( $options.qcSnpHeatmap ) == "True" - --qc-snp-heatmap - #end if - #if str( $options.qcSnpHeatmap ) == "True" - --qc-snp-heatmap - #end if - #if str( $options.qcSnpBoxplot ) == "True" - --qc-snp-boxplot - #end if - #if str( $options.qcSnpBarplot ) == "True" - --qc-snp-barplot - #end if - #if str( $options.qcSampleBatchSize ) != "" - --qc-sample-batch-size="$options.qcSampleBatchSize" - #end if - #if str( $options.filteringContextRemoval ) != "" - --filtering-context-removal="$options.filteringContextRemoval" - #end if - #if str( $options.filteringSnp ) == "True" - --filtering-snp - #end if - #if str( $options.filteringSnpFrequency ) != "" - --filtering-snp-frequency="$options.filteringSnpFrequency" - #end if - #if str( $options.filteringSnpAccepted ) != "" - --filtering-snp-accepted="$options.filteringSnpAccepted" - #end if - #if str( $options.filteringSexChromosomesRemoval ) == "True" - --filtering-sex-chromosomes-removal - #end if - #if str( $options.filteringMissingValueQuantile ) != "" - --filtering-missing-value-quantile="$options.filteringMissingValueQuantile" - #end if - #if str( $options.filteringCoverageThreshold ) != "" - --filtering-coverage-threshold="$options.filteringCoverageThreshold" - #end if - #if str( $options.filteringLowCoverageMasking ) == "True" - --filtering-low-coverage-masking - #end if - #if str( $options.filteringHighCoverageOutliers ) == "True" - --filtering-high-coverage-outliers - #end if - #if str( $options.filteringGreedycut ) == "True" - --filtering-greedycut - #end if - #if str( $options.filteringGreedycutPvalueThreshold ) != "" - --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold" - #end if - #if str( $options.filteringGreedycutRcTies ) != "" - --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies" - #end if - #if str( $options.filteringDeviationThreshold ) != "" - --filtering-deviation-threshold="$options.filteringDeviationThreshold" - #end if - #if str( $options.batch ) == "True" - --batch - #end if - #if str( $options.batchDreductionColumns ) != "" - --batch-dreduction-columns="$options.batchDreductionColumns" - #end if - #if str( $options.batchPrincipalComponents ) != "" - --batch-principal-components="$options.batchPrincipalComponents" - #end if - #if str( $options.batchCorrelationColumns ) != "" - --batch-correlation-columns="$options.batchCorrelationColumns" - #end if - #if str( $options.batchCorrelationPvalueThreshold ) != "" - --batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold" - #end if - #if str( $options.batchCorrelationPermutations ) != "" - --batch-correlation-permutations="$options.batchCorrelationPermutations" - #end if - #if str( $options.batchCorrelationQc ) == "True" - --batch-correlation-qc - #end if - #if str( $options.profiles ) == "True" - --profiles - #end if - #if str( $options.profilesBetaDistribution ) == "True" - --profiles-beta-distribution - #end if - #if str( $options.profilesIntersample ) == "True" - --profiles-intersample - #end if - #if str( $options.profilesDeviationPlots ) == "True" - --profiles-deviation-plots - #end if - #if str( $options.profilesColumns ) != "" - --profiles-columns="$options.profilesColumns" - #end if - #if str( $options.profilesClustering ) == "True" - --profiles-clustering - #end if - #if str( $options.profilesClusteringTopProbes ) != "" - --profiles-clustering-top-probes="$options.profilesClusteringTopProbes" - #end if - #if str( $options.regionProfilesTypes ) != "" - --region-profiles-types="$options.regionProfilesTypes" - #end if - #if str( $options.differential ) == "True" - --differential - #end if - #if str( $options.differentialPermutations ) != "" - --differential-permutations="$options.differentialPermutations" - #end if - #if str( $options.differentialComparisonColumns ) != "" - --differential-comparison-columns="$options.differentialComparisonColumns" - #end if - #if str( $options.differentialComparisonColumnsAllPairwise ) != "" - --differential-comparison-columns-all-pairwise="$options.differentialComparisonColumnsAllPairwise" - #end if - #if str( $options.differentialEnrichment ) == "True" - --differential-enrichment - #end if - #if str( $options.exportToUcsc ) != "" - --export-to-ucsc="$options.exportToUcsc" - #end if - #if str( $options.exportToBed ) == "True" - --export-to-bed - #end if - #if str( $options.exportToCsv ) == "True" - --export-to-csv - #end if - #if str( $options.exportTypes ) != "" - --export-types="$options.exportTypes" - #end if - #if str( $options.colors3Gradient ) != "" - --colors-3-gradient="$options.colors3Gradient" - #end if - #if str( $options.loggingMemory ) == "True" - --logging-memory - #end if - #end if - </command> - <inputs> - <conditional name="inputDataSelector"> - <param name="dataType" type="select" label="Data Type"> - <option value="tables">Tabular data</option> - <option value="idats">IDAT files</option> - <option value="gsreport">GenomeStudio report</option> - <option value="geo">Gene Expression Omnibus series</option> - <option value="bed">BED files</option> - </param> - <when value="tables"> - <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/> - <param name="betaTable" type="data" format="tabular" label="Table with beta-values"/> - <param name="pvalTable" type="data" format="tabular" label="Table with detection p\-values"/> - </when> - <when value="idats"> - <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File"/> - <conditional name="idatSelector"> - <param name="idatSource" type="select" label="IDAT source"> - <option value="history">Select from history</option> - <option value="repo">Repository on the server</option> - </param> - <when value="repo"> - <param name="idatRepo" type="select" label="Select an IDAT repository"> - <options from_data_table="rnbeads_repos"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No repositories are available" /> - </options> - </param> - </when> - <when value="history"> - <repeat min="1" name="idatSeries" title="Input IDAT file"> - <param name="idatFile" type="data" format="idat" label="IDAT file"/> - </repeat> - </when> - </conditional> - </when> - <when value="gsreport"> - <param name="gsReportFile" type="data" format="tabular" label="GenomeStudio report" /> - </when> - <when value="geo"> - <param name="geoSeries" type="text" label="GEO series" /> - </when> - <when value="bed"> - <param name="sampleAnnotations" type="data" format="tabular" label="Sample Annotation File" /> - <repeat min="1" name="bedSeries" title="Input BED file"> - <param name="bedFile" type="data" format="bed" label="BED file"/> - </repeat> - </when> - </conditional> - <conditional name="options"> - <param name="optionSet" type="select" label="Options Set"> - <option value="default">Default options</option> - <option value="full">Full option set</option> - </param> - <when value="default" /> - <when value="full"> - <param name="analysisName" type="text" label="analysis.name, character" value=""/> - <param name="logging" type="select" label="logging, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="email" type="text" label="email, character" value=""/> - <param name="assembly" type="text" label="assembly, character" value="hg19"/> - <param name="columnsPairing" type="text" label="columns.pairing, integer vector" value=""/> - <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="regionTypes" type="text" label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/> - <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/> - <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/> - <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/> - <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/> - <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/> - <param name="maxGroupCount" type="text" label="max.group.count, integer" value="8"/> - <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="strandSpecific" type="select" label="strand.specific, logical" value="0"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/> - <param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="loadingDefaultDataType" type="text" label="loading.default.data.type, character" value="idat.dir"/> - <param name="loadingTableSeparator" type="text" label="loading.table.separator, character" value=","/> - <param name="loadingBedStyle" type="text" label="loading.bed.style, character" value="BisSNP"/> - <param name="loadingBedColumns" type="text" label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/> - <param name="loadingBedFrameShift" type="text" label="loading.bed.frame.shift, integer" value="1"/> - <param name="normalizationMethod" type="text" label="normalization.method, character" value="swan"/> - <param name="normalizationBackgroundMethod" type="text" label="normalization.background.method, character" value="methylumi.noob"/> - <param name="qc" type="select" label="qc, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="500"/> - <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/> - <param name="filteringSnp" type="select" label="filtering.snp, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="filteringSnpFrequency" type="text" label="filtering.snp.frequency, double" value="0.01"/> - <param name="filteringSnpAccepted" type="text" label="filtering.snp.accepted, integer" value="2"/> - <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/> - <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/> - <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/> - <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/> - <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/> - <param name="batch" type="select" label="batch, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="batchDreductionColumns" type="text" label="batch.dreduction.columns, integer vector" value=""/> - <param name="batchPrincipalComponents" type="text" label="batch.principal.components, integer" value="8"/> - <param name="batchCorrelationColumns" type="text" label="batch.correlation.columns, integer vector" value=""/> - <param name="batchCorrelationPvalueThreshold" type="text" label="batch.correlation.pvalue.threshold, double" value="0.01"/> - <param name="batchCorrelationPermutations" type="text" label="batch.correlation.permutations, integer" value="10000"/> - <param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="profiles" type="select" label="profiles, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/> - <param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/> - <param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/> - <param name="differential" type="select" label="differential, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/> - <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/> - <param name="differentialComparisonColumnsAllPairwise" type="text" label="differential.comparison.columns.all.pairwise, integer vector" value=""/> - <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/> - <param name="exportToBed" type="select" label="export.to.bed, logical" value="1"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0"> - <option value="True">True</option> - <option value="False">False</option> - </param> - <param name="exportTypes" type="text" label="export.types, character vector" value="sites"/> - <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/> - <param name="loggingMemory" type="select" label="logging.memory, logical" value="0"> - <option value="True">True</option> - <option value="False">False</option> - </param> - </when> - </conditional> - </inputs> - - <outputs> - <data format="html" name="html_file" label="index.html" /> - </outputs> - - <!-- - <tests> - <test> - <param name="input" value="fa_gc_content_input.fa"/> - <output name="out_file1" file="fa_gc_content_output.txt"/> - </test> - </tests> --> - - <help> - RnBeads is an R-package for comprehensive analysis of Illumina Infinium HumanMethylation450 BeadChip data. It extends previous approaches for this type of data analysis by high throughput capabilities, as well as presenting results in a comprehensive, highly interpretable fashion. - </help> - -</tool> \ No newline at end of file
--- a/rnbeads_galaxy_wrapper.sh Fri Jul 05 08:03:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -#!/bin/bash -Rscript --no-save $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* > /tmp/rnbeads.stdout 2>/tmp/rnbeads.stderr -#Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $* -outfile=`echo $* | cut -d\ -f2 | sed -e "s/--output-file=//g"` -echo $outfile -#outdir=`echo $* | sed -e "s/.*--report-dir=\(.*\)[[:blank:]].*/\1/g"` - - -if [ -s /tmp/rnbeads.stderr ] -then - cat /tmp/rnbeads.stdout >&2 - #cat $outdir/analysis.log >&2 - cat /tmp/rnbeads.stderr >&2 - exit 3 -else - echo "<html><body>" >> $outfile - echo "<a href=\"index.html\">RnBeads report</a>" >> $outfile - echo "<br/><br/>Output was generated during the execution:<br/>" >> $outfile - echo "<pre>" >> outfile - cat /tmp/rnbeads.stdout |sed -e "s/$/<br\/>/g" >> $outfile - echo "</pre>" >> outfile - echo "</p>" >> $outfile - echo "</body></html>" >> $outfile - exit 0 -fi \ No newline at end of file
--- a/rnbeads_repos.txt.sample Fri Jul 05 08:03:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -repo1 Repository1 /data/iscan/idats \ No newline at end of file
--- a/tool_data_table_conf.xml.sample Fri Jul 05 08:03:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<tables> - <table name="rnbeads_repos" comment_char="#"> - <columns>id, name, value</columns> - <file path="tool-data/rnbeads_repos.txt" /> - </table> -</tables> \ No newline at end of file
--- a/tool_dependencies.xml Fri Jul 05 08:03:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <set_environment version="1.0"> - <environment_variable name="R_SCRIPTS_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> - <package name="R" version="3.0.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://CRAN.R-project.org/src/base/R-3/R-3.0.0.tar.gz</action> - <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-x=no</action> - <action type="shell_command">make</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - <action type="shell_command">R --no-save <<< "install.packages("getopt"); source('http://rnbeads.mpi-inf.mpg.de')"</action> - </actions> - </install> - <readme> - You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. - </readme> - </package> -</tool_dependency> \ No newline at end of file