Mercurial > repos > artbio > ngsplot
changeset 3:de27d4172d19 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n'
| author | artbio |
|---|---|
| date | Fri, 08 Dec 2017 17:14:03 -0500 |
| parents | 4b4d858c0aa9 |
| children | 9652d08d8441 |
| files | ngs.plot.r ngsplot.xml runNGSplot.pl setenv.sh |
| diffstat | 4 files changed, 112 insertions(+), 769 deletions(-) [+] |
line wrap: on
line diff
--- a/ngs.plot.r Fri Dec 08 09:36:11 2017 -0500 +++ b/ngs.plot.r Fri Dec 08 17:14:03 2017 -0500 @@ -13,7 +13,7 @@ # Program environment variable. progpath <- Sys.getenv('NGSPLOT') if(progpath == "") { - stop("Set environment variable NGSPLOT before run the program. See README + stop("Set environment variable NGSPLOT before run the program. See README for details.\n") } @@ -48,14 +48,13 @@ # args <- unlist(strsplit('-G mm10 -R tss -C K27M_no_stim_3_GATCAG_L006_R1_001Aligned.out.srt.rmdup.bam -O test -Debug 1', ' ')) # Input argument parser. -args.tbl <- parseArgs(args, c('-G', '-C', '-R', '-O')) # see lib/parse.args.r +args.tbl <- parseArgs(args, c('-G', '-C', '-R')) # see lib/parse.args.r if(is.null(args.tbl)){ cmd.help() stop('Error in parsing command line arguments. Stop.\n') } genome <- args.tbl['-G'] reg2plot <- args.tbl['-R'] -oname <- args.tbl['-O'] warning(sprintf("%s", args.tbl)) cat("Configuring variables...") @@ -74,8 +73,8 @@ ctg.tbl <- ConfigTbl(args.tbl, fraglen) # Setup plot-related coordinates and variables. -plotvar.list <- SetupPlotCoord(args.tbl, ctg.tbl, default.tbl, dbfile.tbl, - progpath, genome, reg2plot, inttag, flanksize, +plotvar.list <- SetupPlotCoord(args.tbl, ctg.tbl, default.tbl, dbfile.tbl, + progpath, genome, reg2plot, inttag, flanksize, samprate, galaxy) attach(plotvar.list) @@ -142,7 +141,7 @@ cat("Done\n") ####################################################################### -# Here start to extract coverages for all genomic regions and calculate +# Here start to extract coverages for all genomic regions and calculate # data for plotting. cat("Analyze bam files and calculate coverage") @@ -188,11 +187,11 @@ cat("\nreport reg2plot\n") cat(reg2plot) cat("\n") - result.matrix <- covMatrix(debug, chkidx.list, coord.list[[reg]], rnaseq.gb, - exonmodel, libsize, TRUE, chr.tag, pint, - reg2plot, flanksize, flankfactor, m.pts, f.pts, - bufsize, cov.algo, bam.files[1], sn.inbam, - fraglens[1], map.qual, is.bowtie, + result.matrix <- covMatrix(debug, chkidx.list, coord.list[[reg]], rnaseq.gb, + exonmodel, libsize, TRUE, chr.tag, pint, + reg2plot, flanksize, flankfactor, m.pts, f.pts, + bufsize, cov.algo, bam.files[1], sn.inbam, + fraglens[1], map.qual, is.bowtie, strand.spec=strand.spec) # Rprof(NULL) if(bam.pair) { # calculate background. @@ -206,14 +205,14 @@ # if(class(chr.tag) == 'character') { # stop(sprintf("Read %s error: %s", bam.files[2], chr.tag)) # } - bkg.matrix <- covMatrix(debug, chkidx.list, coord.list[[reg]], rnaseq.gb, - exonmodel, libsize, TRUE, chr.tag, pint, - reg2plot, flanksize, flankfactor, m.pts, f.pts, - bufsize, cov.algo, bam.files[2], sn.inbam, - fraglen2, map.qual, is.bowtie, + bkg.matrix <- covMatrix(debug, chkidx.list, coord.list[[reg]], rnaseq.gb, + exonmodel, libsize, TRUE, chr.tag, pint, + reg2plot, flanksize, flankfactor, m.pts, f.pts, + bufsize, cov.algo, bam.files[2], sn.inbam, + fraglen2, map.qual, is.bowtie, strand.spec=strand.spec) # browser() - result.matrix <- log2((result.matrix + result.pseudo.rpm) / + result.matrix <- log2((result.matrix + result.pseudo.rpm) / (bkg.matrix + bkg.pseudo.rpm)) } @@ -226,7 +225,7 @@ enrichList[[r]] <- result.matrix # Return avg. profile. - regcovMat[, r] <- apply(result.matrix, 2, function(x) mean(x, trim=robust, + regcovMat[, r] <- apply(result.matrix, 2, function(x) mean(x, trim=robust, na.rm=T)) } # browser() @@ -236,7 +235,7 @@ # Add row names to heatmap data. for(i in 1:length(enrichList)) { reg <- ctg.tbl$glist[i] # gene list name. - rownames(enrichList[[i]]) <- paste(coord.list[[reg]]$gname, + rownames(enrichList[[i]]) <- paste(coord.list[[reg]]$gname, coord.list[[reg]]$tid, sep=':') } # Some basic parameters. @@ -250,13 +249,13 @@ #### Average profile plot. #### out.plot <- avgname pdf(out.plot, width=plot.width, height=plot.height, pointsize=font.size) - plotmat(regcovMat, ctg.tbl$title, ctg.tbl$color, bam.pair, xticks, pts, + plotmat(regcovMat, ctg.tbl$title, ctg.tbl$color, bam.pair, xticks, pts, m.pts, f.pts, pint, shade.alp, confiMat, mw, prof.misc) out.dev <- dev.off() #### Heatmap. #### # Setup output device. - hd <- SetupHeatmapDevice(reg.list, uniq.reg, ng.list, pts, font.size, + hd <- SetupHeatmapDevice(reg.list, uniq.reg, ng.list, pts, font.size, unit.width, rr) reg.hei <- hd$reg.hei # list of image heights for unique regions. hm.width <- hd$hm.width # image width. @@ -270,16 +269,16 @@ layout(lay.mat, heights=reg.hei) # Do heatmap plotting. - go.list <- plotheat(reg.list, uniq.reg, enrichList, v.low.cutoff, go.algo, - go.paras, ctg.tbl$title, bam.pair, xticks, flood.frac, - do.plot=T, hm.color=hm.color, color.distr=color.distr, + go.list <- plotheat(reg.list, uniq.reg, enrichList, v.low.cutoff, go.algo, + go.paras, ctg.tbl$title, bam.pair, xticks, flood.frac, + do.plot=T, hm.color=hm.color, color.distr=color.distr, color.scale=color.scale) out.dev <- dev.off() cat("Done\n") } else { - go.list <- plotheat(reg.list, uniq.reg, enrichList, v.low.cutoff, go.algo, - go.paras, ctg.tbl$title, bam.pair, xticks, flood.frac, - do.plot=F, hm.color=hm.color, color.distr=color.distr, + go.list <- plotheat(reg.list, uniq.reg, enrichList, v.low.cutoff, go.algo, + go.paras, ctg.tbl$title, bam.pair, xticks, flood.frac, + do.plot=F, hm.color=hm.color, color.distr=color.distr, color.scale=color.scale) } @@ -302,40 +301,48 @@ for(i in 1:length(enrichList)) { reg <- ctg.tbl$glist[i] # gene list name. out.heat <- file.path(oname1, paste('hm', i, '.txt', sep='')) - write.table(cbind(coord.list[[reg]][, c('gid', 'gname', 'tid', 'strand')], - enrichList[[i]]), + write.table(cbind(coord.list[[reg]][, c('gid', 'gname', 'tid', 'strand')], + enrichList[[i]]), file=out.heat, row.names=F, sep="\t", quote=F) } # Avg. profile R data. prof.dat <- file.path(oname1, 'avgprof.RData') -save(plot.width, plot.height, regcovMat, ctg.tbl, bam.pair, xticks, pts, - m.pts, f.pts, pint, shade.alp, confiMat, mw, prof.misc, se, v.lib.size, +save(plot.width, plot.height, regcovMat, ctg.tbl, bam.pair, xticks, pts, + m.pts, f.pts, pint, shade.alp, confiMat, mw, prof.misc, se, v.lib.size, font.size, file=prof.dat) # Heatmap R data. heat.dat <- file.path(oname1, 'heatmap.RData') -save(reg.list, uniq.reg, ng.list, pts, enrichList, v.low.cutoff, go.algo, - ctg.tbl, bam.pair, xticks, flood.frac, hm.color, unit.width, rr, +save(reg.list, uniq.reg, ng.list, pts, enrichList, v.low.cutoff, go.algo, + ctg.tbl, bam.pair, xticks, flood.frac, hm.color, unit.width, rr, go.list, color.scale, v.lib.size, font.size, go.paras, low.count, - color.distr, + color.distr, file=heat.dat) cat("Done\n") # Wrap results up. cat("Wrapping results up...") cur.dir <- getwd() +cat("cur.dir") +cat(cur.dir) out.dir <- dirname(oname1) +cat("out.dir") +cat(out.dir) out.zip <- basename(oname1) -setwd(out.dir) -if(!zip(paste(out.zip, '.zip', sep=''), out.zip, extras='-q')) { - if(unlink(oname, recursive=T)) { - warning(sprintf("Unable to delete intermediate result folder: %s", - oname)) - } -} -setwd(cur.dir) +cat("out.zip") +cat(out.zip) +#setwd(out.dir) +#cat("Reaching this point without failure") +#zip(paste(out.zip, '.zip', sep=''), out.zip, extras='-q') +zip("data.zip", "data", extras='-q') +#if(!zip(paste(out.zip, '.zip', sep=''), out.zip, extras='-q')) { +# if(unlink(oname, recursive=T)) { +# warning(sprintf("Unable to delete intermediate result folder: %s", +# oname)) +# } +#} +#setwd(cur.dir) cat("Done\n") cat("All done. Cheers!\n") -
--- a/ngsplot.xml Fri Dec 08 09:36:11 2017 -0500 +++ b/ngsplot.xml Fri Dec 08 17:14:03 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="ngsplot" name="ngsplot" version="0.2.0"> +<tool id="ngsplot" name="ngsplot" version="0.3.0"> <description>visualize NGS samples at functional genomic regions - beta</description> <requirements> <requirement type="package" version="1.17.1=r3.3.2_1">r-catools</requirement> @@ -13,13 +13,13 @@ export NGSPLOT="$__tool_directory__" && printenv && #if $numsamples.numsamples2 == "1": - perl "$__tool_directory__"/runNGSplot.pl - $genome_name - $genomic_region_source_type.genomic_region - $genomic_region_source_type.further_information - $genomic_region_source_type.interval_size - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size + perl "$__tool_directory__"/runNGSplot.pl + $genome_name + $genomic_region_source_type.genomic_region + $genomic_region_source_type.further_information + $genomic_region_source_type.interval_size + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option + $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size $numsamples.numsamples2 $numsamples.usepair.usepair1 @@ -44,674 +44,9 @@ $flooding_fraction $smooth_method $shaded_area - $out_zip $out_avg_png $out_hm_png - -#else if $numsamples.numsamples2 == "2": - perl "$__tool_directory__"/runNGSplot.pl - $genome_name - $genomic_region_source_type.genomic_region - $genomic_region_source_type.further_information - $genomic_region_source_type.interval_size - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size - $numsamples.numsamples2 - $numsamples.usepair.usepair1 - - $numsamples.usepair.bamfile1 - $numsamples.usepair.reffile1 - $numsamples.usepair.genelist1.usegenelist1 - $numsamples.usepair.genelist1.genelist1 - $numsamples.usepair.title1 - $numsamples.usepair.fraglen1 - $numsamples.usepair.linecol1 - - $numsamples.usepair.bamfile2 - $numsamples.usepair.reffile2 - $numsamples.usepair.genelist2.usegenelist2 - $numsamples.usepair.genelist2.genelist2 - $numsamples.usepair.title2 - $numsamples.usepair.fraglen2 - $numsamples.usepair.linecol2 - - $gene_database - $randomly_sample - $GO.gene_order - $GO.KNC - $GO.MIT - $GO.NRS - $chunk_size - $quality_requirement - $standard_error - $radius_size - $flooding_fraction - $smooth_method - $shaded_area - $out_zip $out_avg_png $out_hm_png - -#else if $numsamples.numsamples2 == "3": - perl "$__tool_directory__"/runNGSplot.pl - $genome_name - $genomic_region_source_type.genomic_region - $genomic_region_source_type.further_information - $genomic_region_source_type.interval_size - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size - $numsamples.numsamples2 - $numsamples.usepair.usepair1 - - $numsamples.usepair.bamfile1 - $numsamples.usepair.reffile1 - $numsamples.usepair.genelist1.usegenelist1 - $numsamples.usepair.genelist1.genelist1 - $numsamples.usepair.title1 - $numsamples.usepair.fraglen1 - $numsamples.usepair.linecol1 - - $numsamples.usepair.bamfile2 - $numsamples.usepair.reffile2 - $numsamples.usepair.genelist2.usegenelist2 - $numsamples.usepair.genelist2.genelist2 - $numsamples.usepair.title2 - $numsamples.usepair.fraglen2 - $numsamples.usepair.linecol2 - - $numsamples.usepair.bamfile3 - $numsamples.usepair.reffile3 - $numsamples.usepair.genelist3.usegenelist3 - $numsamples.usepair.genelist3.genelist3 - $numsamples.usepair.title3 - $numsamples.usepair.fraglen3 - $numsamples.usepair.linecol3 - - $gene_database - $randomly_sample - $GO.gene_order - $GO.KNC - $GO.MIT - $GO.NRS - $chunk_size - $quality_requirement - $standard_error - $radius_size - $flooding_fraction - $smooth_method - $shaded_area - $out_zip $out_avg_png $out_hm_png - -#else if $numsamples.numsamples2 == "4": - perl "$__tool_directory__"/runNGSplot.pl - $genome_name - $genomic_region_source_type.genomic_region - $genomic_region_source_type.further_information - $genomic_region_source_type.interval_size - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size - $numsamples.numsamples2 - $numsamples.usepair.usepair1 - - $numsamples.usepair.bamfile1 - $numsamples.usepair.reffile1 - $numsamples.usepair.genelist1.usegenelist1 - $numsamples.usepair.genelist1.genelist1 - $numsamples.usepair.title1 - $numsamples.usepair.fraglen1 - $numsamples.usepair.linecol1 - - $numsamples.usepair.bamfile2 - $numsamples.usepair.reffile2 - $numsamples.usepair.genelist2.usegenelist2 - $numsamples.usepair.genelist2.genelist2 - $numsamples.usepair.title2 - $numsamples.usepair.fraglen2 - $numsamples.usepair.linecol2 - - $numsamples.usepair.bamfile3 - $numsamples.usepair.reffile3 - $numsamples.usepair.genelist3.usegenelist3 - $numsamples.usepair.genelist3.genelist3 - $numsamples.usepair.title3 - $numsamples.usepair.fraglen3 - $numsamples.usepair.linecol3 - - $numsamples.usepair.bamfile4 - $numsamples.usepair.reffile4 - $numsamples.usepair.genelist4.usegenelist4 - $numsamples.usepair.genelist4.genelist4 - $numsamples.usepair.title4 - $numsamples.usepair.fraglen4 - $numsamples.usepair.linecol4 - - $gene_database - $randomly_sample - $GO.gene_order - $GO.KNC - $GO.MIT - $GO.NRS - $chunk_size - $quality_requirement - $standard_error - $radius_size - $flooding_fraction - $smooth_method - $shaded_area - $out_zip $out_avg_png $out_hm_png - -#else if $numsamples.numsamples2 == "5": - perl "$__tool_directory__"/runNGSplot.pl - $genome_name - $genomic_region_source_type.genomic_region - $genomic_region_source_type.further_information - $genomic_region_source_type.interval_size - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size - $numsamples.numsamples2 - $numsamples.usepair.usepair1 - - $numsamples.usepair.bamfile1 - $numsamples.usepair.reffile1 - $numsamples.usepair.genelist1.usegenelist1 - $numsamples.usepair.genelist1.genelist1 - $numsamples.usepair.title1 - $numsamples.usepair.fraglen1 - $numsamples.usepair.linecol1 - - $numsamples.usepair.bamfile2 - $numsamples.usepair.reffile2 - $numsamples.usepair.genelist2.usegenelist2 - $numsamples.usepair.genelist2.genelist2 - $numsamples.usepair.title2 - $numsamples.usepair.fraglen2 - $numsamples.usepair.linecol2 - - $numsamples.usepair.bamfile3 - $numsamples.usepair.reffile3 - $numsamples.usepair.genelist3.usegenelist3 - $numsamples.usepair.genelist3.genelist3 - $numsamples.usepair.title3 - $numsamples.usepair.fraglen3 - $numsamples.usepair.linecol3 - - $numsamples.usepair.bamfile4 - $numsamples.usepair.reffile4 - $numsamples.usepair.genelist4.usegenelist4 - $numsamples.usepair.genelist4.genelist4 - $numsamples.usepair.title4 - $numsamples.usepair.fraglen4 - $numsamples.usepair.linecol4 - - $numsamples.usepair.bamfile5 - $numsamples.usepair.reffile5 - $numsamples.usepair.genelist5.usegenelist5 - $numsamples.usepair.genelist5.genelist5 - $numsamples.usepair.title5 - $numsamples.usepair.fraglen5 - $numsamples.usepair.linecol5 - - $gene_database - $randomly_sample - $GO.gene_order - $GO.KNC - $GO.MIT - $GO.NRS - $chunk_size - $quality_requirement - $standard_error - $radius_size - $flooding_fraction - $smooth_method - $shaded_area - $out_zip $out_avg_png $out_hm_png - -#else if $numsamples.numsamples2 == "6": - perl "$__tool_directory__"/runNGSplot.pl - $genome_name - $genomic_region_source_type.genomic_region - $genomic_region_source_type.further_information - $genomic_region_source_type.interval_size - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size - $numsamples.numsamples2 - $numsamples.usepair.usepair1 - - $numsamples.usepair.bamfile1 - $numsamples.usepair.reffile1 - $numsamples.usepair.genelist1.usegenelist1 - $numsamples.usepair.genelist1.genelist1 - $numsamples.usepair.title1 - $numsamples.usepair.fraglen1 - $numsamples.usepair.linecol1 - - $numsamples.usepair.bamfile2 - $numsamples.usepair.reffile2 - $numsamples.usepair.genelist2.usegenelist2 - $numsamples.usepair.genelist2.genelist2 - $numsamples.usepair.title2 - $numsamples.usepair.fraglen2 - $numsamples.usepair.linecol2 - - $numsamples.usepair.bamfile3 - $numsamples.usepair.reffile3 - $numsamples.usepair.genelist3.usegenelist3 - $numsamples.usepair.genelist3.genelist3 - $numsamples.usepair.title3 - $numsamples.usepair.fraglen3 - $numsamples.usepair.linecol3 - - $numsamples.usepair.bamfile4 - $numsamples.usepair.reffile4 - $numsamples.usepair.genelist4.usegenelist4 - $numsamples.usepair.genelist4.genelist4 - $numsamples.usepair.title4 - $numsamples.usepair.fraglen4 - $numsamples.usepair.linecol4 - - $numsamples.usepair.bamfile5 - $numsamples.usepair.reffile5 - $numsamples.usepair.genelist5.usegenelist5 - $numsamples.usepair.genelist5.genelist5 - $numsamples.usepair.title5 - $numsamples.usepair.fraglen5 - $numsamples.usepair.linecol5 - - $numsamples.usepair.bamfile6 - $numsamples.usepair.reffile6 - $numsamples.usepair.genelist6.usegenelist6 - $numsamples.usepair.genelist6.genelist6 - $numsamples.usepair.title6 - $numsamples.usepair.fraglen6 - $numsamples.usepair.linecol6 - - $gene_database - $randomly_sample - $GO.gene_order - $GO.KNC - $GO.MIT - $GO.NRS - $chunk_size - $quality_requirement - $standard_error - $radius_size - $flooding_fraction - $smooth_method - $shaded_area - $out_zip $out_avg_png $out_hm_png - -#else if $numsamples.numsamples2 == "7": - perl "$__tool_directory__"/runNGSplot.pl - $genome_name - $genomic_region_source_type.genomic_region - $genomic_region_source_type.further_information - $genomic_region_source_type.interval_size - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size - $numsamples.numsamples2 - $numsamples.usepair.usepair1 - - $numsamples.usepair.bamfile1 - $numsamples.usepair.reffile1 - $numsamples.usepair.genelist1.usegenelist1 - $numsamples.usepair.genelist1.genelist1 - $numsamples.usepair.title1 - $numsamples.usepair.fraglen1 - $numsamples.usepair.linecol1 - - $numsamples.usepair.bamfile2 - $numsamples.usepair.reffile2 - $numsamples.usepair.genelist2.usegenelist2 - $numsamples.usepair.genelist2.genelist2 - $numsamples.usepair.title2 - $numsamples.usepair.fraglen2 - $numsamples.usepair.linecol2 - - $numsamples.usepair.bamfile3 - $numsamples.usepair.reffile3 - $numsamples.usepair.genelist3.usegenelist3 - $numsamples.usepair.genelist3.genelist3 - $numsamples.usepair.title3 - $numsamples.usepair.fraglen3 - $numsamples.usepair.linecol3 - - $numsamples.usepair.bamfile4 - $numsamples.usepair.reffile4 - $numsamples.usepair.genelist4.usegenelist4 - $numsamples.usepair.genelist4.genelist4 - $numsamples.usepair.title4 - $numsamples.usepair.fraglen4 - $numsamples.usepair.linecol4 - - $numsamples.usepair.bamfile5 - $numsamples.usepair.reffile5 - $numsamples.usepair.genelist5.usegenelist5 - $numsamples.usepair.genelist5.genelist5 - $numsamples.usepair.title5 - $numsamples.usepair.fraglen5 - $numsamples.usepair.linecol5 - - $numsamples.usepair.bamfile6 - $numsamples.usepair.reffile6 - $numsamples.usepair.genelist6.usegenelist6 - $numsamples.usepair.genelist6.genelist6 - $numsamples.usepair.title6 - $numsamples.usepair.fraglen6 - $numsamples.usepair.linecol6 - - $numsamples.usepair.bamfile7 - $numsamples.usepair.reffile7 - $numsamples.usepair.genelist7.usegenelist7 - $numsamples.usepair.genelist7.genelist7 - $numsamples.usepair.title7 - $numsamples.usepair.fraglen7 - $numsamples.usepair.linecol7 - - $gene_database - $randomly_sample - $GO.gene_order - $GO.KNC - $GO.MIT - $GO.NRS - $chunk_size - $quality_requirement - $standard_error - $radius_size - $flooding_fraction - $smooth_method - $shaded_area - $out_zip $out_avg_png $out_hm_png - -#else if $numsamples.numsamples2 == "8": - perl "$__tool_directory__"/runNGSplot.pl - $genome_name - $genomic_region_source_type.genomic_region - $genomic_region_source_type.further_information - $genomic_region_source_type.interval_size - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size - $numsamples.numsamples2 - $numsamples.usepair.usepair1 - - $numsamples.usepair.bamfile1 - $numsamples.usepair.reffile1 - $numsamples.usepair.genelist1.usegenelist1 - $numsamples.usepair.genelist1.genelist1 - $numsamples.usepair.title1 - $numsamples.usepair.fraglen1 - $numsamples.usepair.linecol1 - - $numsamples.usepair.bamfile2 - $numsamples.usepair.reffile2 - $numsamples.usepair.genelist2.usegenelist2 - $numsamples.usepair.genelist2.genelist2 - $numsamples.usepair.title2 - $numsamples.usepair.fraglen2 - $numsamples.usepair.linecol2 - - $numsamples.usepair.bamfile3 - $numsamples.usepair.reffile3 - $numsamples.usepair.genelist3.usegenelist3 - $numsamples.usepair.genelist3.genelist3 - $numsamples.usepair.title3 - $numsamples.usepair.fraglen3 - $numsamples.usepair.linecol3 - - $numsamples.usepair.bamfile4 - $numsamples.usepair.reffile4 - $numsamples.usepair.genelist4.usegenelist4 - $numsamples.usepair.genelist4.genelist4 - $numsamples.usepair.title4 - $numsamples.usepair.fraglen4 - $numsamples.usepair.linecol4 - - $numsamples.usepair.bamfile5 - $numsamples.usepair.reffile5 - $numsamples.usepair.genelist5.usegenelist5 - $numsamples.usepair.genelist5.genelist5 - $numsamples.usepair.title5 - $numsamples.usepair.fraglen5 - $numsamples.usepair.linecol5 - - $numsamples.usepair.bamfile6 - $numsamples.usepair.reffile6 - $numsamples.usepair.genelist6.usegenelist6 - $numsamples.usepair.genelist6.genelist6 - $numsamples.usepair.title6 - $numsamples.usepair.fraglen6 - $numsamples.usepair.linecol6 - - $numsamples.usepair.bamfile7 - $numsamples.usepair.reffile7 - $numsamples.usepair.genelist7.usegenelist7 - $numsamples.usepair.genelist7.genelist7 - $numsamples.usepair.title7 - $numsamples.usepair.fraglen7 - $numsamples.usepair.linecol7 - - $numsamples.usepair.bamfile8 - $numsamples.usepair.reffile8 - $numsamples.usepair.genelist8.usegenelist8 - $numsamples.usepair.genelist8.genelist8 - $numsamples.usepair.title8 - $numsamples.usepair.fraglen8 - $numsamples.usepair.linecol8 - - $gene_database - $randomly_sample - $GO.gene_order - $GO.KNC - $GO.MIT - $GO.NRS - $chunk_size - $quality_requirement - $standard_error - $radius_size - $flooding_fraction - $smooth_method - $shaded_area - $out_zip $out_avg_png $out_hm_png - -#else if $numsamples.numsamples2 == "9": - perl "$__tool_directory__"/runNGSplot.pl - $genome_name - $genomic_region_source_type.genomic_region - $genomic_region_source_type.further_information - $genomic_region_source_type.interval_size - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size - $numsamples.numsamples2 - $numsamples.usepair.usepair1 - - $numsamples.usepair.bamfile1 - $numsamples.usepair.reffile1 - $numsamples.usepair.genelist1.usegenelist1 - $numsamples.usepair.genelist1.genelist1 - $numsamples.usepair.title1 - $numsamples.usepair.fraglen1 - $numsamples.usepair.linecol1 - - $numsamples.usepair.bamfile2 - $numsamples.usepair.reffile2 - $numsamples.usepair.genelist2.usegenelist2 - $numsamples.usepair.genelist2.genelist2 - $numsamples.usepair.title2 - $numsamples.usepair.fraglen2 - $numsamples.usepair.linecol2 - - $numsamples.usepair.bamfile3 - $numsamples.usepair.reffile3 - $numsamples.usepair.genelist3.usegenelist3 - $numsamples.usepair.genelist3.genelist3 - $numsamples.usepair.title3 - $numsamples.usepair.fraglen3 - $numsamples.usepair.linecol3 - - $numsamples.usepair.bamfile4 - $numsamples.usepair.reffile4 - $numsamples.usepair.genelist4.usegenelist4 - $numsamples.usepair.genelist4.genelist4 - $numsamples.usepair.title4 - $numsamples.usepair.fraglen4 - $numsamples.usepair.linecol4 - - $numsamples.usepair.bamfile5 - $numsamples.usepair.reffile5 - $numsamples.usepair.genelist5.usegenelist5 - $numsamples.usepair.genelist5.genelist5 - $numsamples.usepair.title5 - $numsamples.usepair.fraglen5 - $numsamples.usepair.linecol5 - - $numsamples.usepair.bamfile6 - $numsamples.usepair.reffile6 - $numsamples.usepair.genelist6.usegenelist6 - $numsamples.usepair.genelist6.genelist6 - $numsamples.usepair.title6 - $numsamples.usepair.fraglen6 - $numsamples.usepair.linecol6 - - $numsamples.usepair.bamfile7 - $numsamples.usepair.reffile7 - $numsamples.usepair.genelist7.usegenelist7 - $numsamples.usepair.genelist7.genelist7 - $numsamples.usepair.title7 - $numsamples.usepair.fraglen7 - $numsamples.usepair.linecol7 - - $numsamples.usepair.bamfile8 - $numsamples.usepair.reffile8 - $numsamples.usepair.genelist8.usegenelist8 - $numsamples.usepair.genelist8.genelist8 - $numsamples.usepair.title8 - $numsamples.usepair.fraglen8 - $numsamples.usepair.linecol8 - - $numsamples.usepair.bamfile9 - $numsamples.usepair.reffile9 - $numsamples.usepair.genelist9.usegenelist9 - $numsamples.usepair.genelist9.genelist9 - $numsamples.usepair.title9 - $numsamples.usepair.fraglen9 - $numsamples.usepair.linecol9 - - $gene_database - $randomly_sample - $GO.gene_order - $GO.KNC - $GO.MIT - $GO.NRS - $chunk_size - $quality_requirement - $standard_error - $radius_size - $flooding_fraction - $smooth_method - $shaded_area - $out_zip $out_avg_png $out_hm_png - -#else if $numsamples.numsamples2 == "10": - perl "$__tool_directory__"/runNGSplot.pl - $genome_name - $genomic_region_source_type.genomic_region - $genomic_region_source_type.further_information - $genomic_region_source_type.interval_size - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option - $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size - $numsamples.numsamples2 - $numsamples.usepair.usepair1 - - $numsamples.usepair.bamfile1 - $numsamples.usepair.reffile1 - $numsamples.usepair.genelist1.usegenelist1 - $numsamples.usepair.genelist1.genelist1 - $numsamples.usepair.title1 - $numsamples.usepair.fraglen1 - $numsamples.usepair.linecol1 - - $numsamples.usepair.bamfile2 - $numsamples.usepair.reffile2 - $numsamples.usepair.genelist2.usegenelist2 - $numsamples.usepair.genelist2.genelist2 - $numsamples.usepair.title2 - $numsamples.usepair.fraglen2 - $numsamples.usepair.linecol2 - - $numsamples.usepair.bamfile3 - $numsamples.usepair.reffile3 - $numsamples.usepair.genelist3.usegenelist3 - $numsamples.usepair.genelist3.genelist3 - $numsamples.usepair.title3 - $numsamples.usepair.fraglen3 - $numsamples.usepair.linecol3 - - $numsamples.usepair.bamfile4 - $numsamples.usepair.reffile4 - $numsamples.usepair.genelist4.usegenelist4 - $numsamples.usepair.genelist4.genelist4 - $numsamples.usepair.title4 - $numsamples.usepair.fraglen4 - $numsamples.usepair.linecol4 - - $numsamples.usepair.bamfile5 - $numsamples.usepair.reffile5 - $numsamples.usepair.genelist5.usegenelist5 - $numsamples.usepair.genelist5.genelist5 - $numsamples.usepair.title5 - $numsamples.usepair.fraglen5 - $numsamples.usepair.linecol5 - - $numsamples.usepair.bamfile6 - $numsamples.usepair.reffile6 - $numsamples.usepair.genelist6.usegenelist6 - $numsamples.usepair.genelist6.genelist6 - $numsamples.usepair.title6 - $numsamples.usepair.fraglen6 - $numsamples.usepair.linecol6 - - $numsamples.usepair.bamfile7 - $numsamples.usepair.reffile7 - $numsamples.usepair.genelist7.usegenelist7 - $numsamples.usepair.genelist7.genelist7 - $numsamples.usepair.title7 - $numsamples.usepair.fraglen7 - $numsamples.usepair.linecol7 - - $numsamples.usepair.bamfile8 - $numsamples.usepair.reffile8 - $numsamples.usepair.genelist8.usegenelist8 - $numsamples.usepair.genelist8.genelist8 - $numsamples.usepair.title8 - $numsamples.usepair.fraglen8 - $numsamples.usepair.linecol8 - - $numsamples.usepair.bamfile9 - $numsamples.usepair.reffile9 - $numsamples.usepair.genelist9.usegenelist9 - $numsamples.usepair.genelist9.genelist9 - $numsamples.usepair.title9 - $numsamples.usepair.fraglen9 - $numsamples.usepair.linecol9 - - $numsamples.usepair.bamfile10 - $numsamples.usepair.reffile10 - $numsamples.usepair.genelist10.usegenelist10 - $numsamples.usepair.genelist10.genelist10 - $numsamples.usepair.title10 - $numsamples.usepair.fraglen10 - $numsamples.usepair.linecol10 - - $gene_database - $randomly_sample - $GO.gene_order - $GO.KNC - $GO.MIT - $GO.NRS - $chunk_size - $quality_requirement - $standard_error - $radius_size - $flooding_fraction - $smooth_method - $shaded_area - $out_zip $out_avg_png $out_hm_png - + ## $out_zip + $out_avg_png $out_hm_png && + tar -cf $out_tar data/ #end if ]]></command> @@ -720,7 +55,8 @@ <--> <inputs> - <param type="text" value="mm9" name="genome_name" label="Genome" help="(hg19, mm9, rn4, or other genomes supported by your NGS.plot installation)" > + <param type="select" name="genome_name" label="Genome" help="Select Genome (only hg38 supported in this draft)"> + <option value="hg38">hg38</option> </param> <conditional name="genomic_region_source_type"> <param type="select" name="genomic_region" label="Genomic region" help=""> @@ -732,7 +68,7 @@ <option value="bed">Customized bed file</option> </param> - <when value="tss"> + <when value="tss"> <param type="select" name="further_information" label="Further information: Not required for TSS"> <option value="na">Not Required</option> </param> @@ -748,11 +84,11 @@ <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> </when> <!--when value="flanking_floating_size"> - <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> + <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> </when--> </conditional> - </when> - <when value="tes"> + </when> + <when value="tes"> <param type="select" name="further_information" label="Further information: Not required for TES"> <option value="na">Not Required</option> </param> @@ -768,11 +104,11 @@ <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> </when> <!--when value="flanking_floating_size"> - <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> + <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> </when--> </conditional> - </when> - <when value="genebody"> + </when> + <when value="genebody"> <param type="select" name="further_information" label="You selected Genebody, further information can be provided for specific regions to plot"> <option value="chipseq">ChIP-seq</option> <option value="rnaseq">RNA-seq</option> @@ -793,9 +129,9 @@ <when value="flanking_floating_size"> <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> </when> - </conditional> + </conditional> </when> - <when value="exon"> + <when value="exon"> <param type="select" name="further_information" label="You selected Exon, further information can be provided for specific regions to plot"> <option value="canonical">Canonical</option> <option value="variant">Variant</option> @@ -823,7 +159,7 @@ </when> </conditional> </when> - <when value="cgi"> + <when value="cgi"> <param type="select" name="further_information" label="You select CGI, further information can be provided for specific regions to plot"> <option value="ProximalPromoter">ProximalPromoter</option> <option value="Genebody">GeneBody</option> @@ -848,11 +184,11 @@ <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> </when> <when value="flanking_floating_size"> - <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> + <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> </when> </conditional> - </when> - <when value="bed"> + </when> + <when value="bed"> <param type="select" name="further_information" label="Further information: Not required for bed input"> <option value="na">Not Required</option> </param> @@ -870,10 +206,10 @@ <param name="flanking_region_size" size="30" type="text" value="1000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> </when> <when value="flanking_floating_size"> - <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> + <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> </when> </conditional> - </when> + </when> </conditional> @@ -891,60 +227,60 @@ <option value="10">10</option> --> </param> - <when value="1"> + <when value="1"> <conditional name="usepair"> <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> <option value="no">No</option> <option value="yes">Yes</option> </param> - <when value="no"> + <when value="no"> <!-- START: 1 sample, no refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> - <param type="hidden" name="reffile1" value="na"/> + <param type="hidden" name="reffile1" value="na"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> - <when value="no"> + <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> - <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> - <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> - <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 1 sample, no refpairs, entry 1--> - </when> - <when value="yes"> + </when> + <when value="yes"> <!-- START: 1 sample, yes refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> - <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> + <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> - <when value="no"> + <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> - <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> - <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> - <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> + <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> + <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> + <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 1 sample, yes refpairs, entry 1--> - </when> + </when> </conditional> - </when> + </when> </conditional> - + <param type="select" name="gene_database" label="Supported gene database: RefSeq, Ensembl"> <option value="ensembl">Ensembl</option> <option value="refseq">RefSeq</option> @@ -1021,6 +357,6 @@ <outputs> <data format="pdf" name="out_avg_png" /> <data format="pdf" name="out_hm_png" /> - <data format="zip" name="out_zip"/> + <data format="tar" name="out_tar"/> </outputs> </tool>
--- a/runNGSplot.pl Fri Dec 08 09:36:11 2017 -0500 +++ b/runNGSplot.pl Fri Dec 08 17:14:03 2017 -0500 @@ -32,7 +32,7 @@ my $genelist=shift(@inputs); my $title=shift(@inputs); my $fraglen=shift(@inputs); - my $color=shift(@inputs); + my $color=shift(@inputs); if ($usepairs eq 'yes') { syswrite(FILE, "$bamfile\:$reffile\t$genelist\t$title\t$fraglen\t$color\n"); }else { @@ -54,7 +54,7 @@ my $flooding_fraction = shift(@inputs); my $smooth_method = shift(@inputs); my $shaded_area = shift(@inputs); -my $out_name = shift(@inputs); +# my $out_name = shift(@inputs); my $out_avg_name = shift(@inputs); my $out_hm_name = shift(@inputs); @@ -62,7 +62,7 @@ my $G = $genome_name; my $R = $genomic_region_source_type__genomic_region; my $C = $outfile; -my $O = $out_name; +# my $O = $out_name; my $O2 = $out_avg_name; my $O3 = $out_hm_name; my $F = $genomic_region_source_type__further_information; @@ -94,33 +94,31 @@ my $NGSPLOT = $ENV{"NGSPLOT"}; my $cmd=''; if (($R eq 'tss')||($R eq 'tes')) { - $cmd = "Rscript $NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; + $cmd = "Rscript $NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; }elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_region_size') { if ($IN eq 'automatic') { - $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; + $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; }else { - $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN >> $logfile 2>&1"; + $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN >> $logfile 2>&1"; } }elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_floating_size') { if ($IN eq 'automatic') { - $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; + $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1"; }else { - $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN >> $logfile 2>&1"; + $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN >> $logfile 2>&1"; } } print("$cmd\n"); -my $cmd2="cp data.zip $O"; -my $cmd3="rm $outfile"; +#my $cmd2="cp data.zip $O"; +#my $cmd3="rm $outfile"; syswrite(FILE2, "\n$cmd\n"); -syswrite(FILE2, "\n$cmd2\n"); -syswrite(FILE2, "\n$cmd3\n"); +#syswrite(FILE2, "\n$cmd2\n"); +#syswrite(FILE2, "\n$cmd3\n"); # print STDERR "cmd: $cmd\n"; system($cmd); -system($cmd2); -system($cmd3); +#system($cmd2); +#system($cmd3); close(FILE2); - -