Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
comparison readmap.xml @ 2:ebfc73c72652 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
author | mvdbeek |
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date | Wed, 03 Feb 2016 09:20:34 -0500 |
parents | e4874d1ae69d |
children | 4efe210c91f3 |
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1:e4874d1ae69d | 2:ebfc73c72652 |
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1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.5"> | 1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.2"> |
2 <description>from sRbowtie aligment</description> | 2 <description>from sRbowtie aligment</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.12.7">bowtie</requirement> | 4 <requirement type="package" version="0.12.7">bowtie</requirement> |
5 <requirement type="package" version="0.7.7">pysam</requirement> | 5 <requirement type="package" version="0.7.7">pysam</requirement> |
6 <requirement type="package" version="3.1.2">R</requirement> | 6 <requirement type="package" version="3.1.2">R</requirement> |
76 <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/> | 76 <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/> |
77 <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/> | 77 <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/> |
78 <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/> | 78 <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/> |
79 <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/> | 79 <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/> |
80 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/> | 80 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/> |
81 <param name="yrange" type="integer" size="3" value="0" label="y axis range for readmaps. 0 means auto-scaling."/> | |
81 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?"> | 82 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?"> |
82 <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/> | 83 <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/> |
83 </param> | 84 </param> |
84 </inputs> | 85 </inputs> |
85 <configfiles> | 86 <configfiles> |
165 pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width) | 166 pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width) |
166 for (i in seq(1,n_genes,rows_per_page)) { | 167 for (i in seq(1,n_genes,rows_per_page)) { |
167 start=i | 168 start=i |
168 end=i+rows_per_page-1 | 169 end=i+rows_per_page-1 |
169 if (end>n_genes) {end=n_genes} | 170 if (end>n_genes) {end=n_genes} |
170 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) | 171 if (${yrange} == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { |
172 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}) , par.settings=par.settings.readmap)) } | |
171 args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1, | 173 args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1, |
172 main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"), | 174 main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"), |
173 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90) | 175 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90) |
174 #sub=textGrob("readmap coordinates", gp=gpar(cex=.75), just="bottom") | 176 #sub=textGrob("readmap coordinates", gp=gpar(cex=.75), just="bottom") |
175 ) | 177 ) |
198 pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width) | 200 pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width) |
199 for (i in seq(1,n_genes,rows_per_page/2)) { | 201 for (i in seq(1,n_genes,rows_per_page/2)) { |
200 start=i | 202 start=i |
201 end=i+rows_per_page/2-1 | 203 end=i+rows_per_page/2-1 |
202 if (end>n_genes) {end=n_genes} | 204 if (end>n_genes) {end=n_genes} |
203 read_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.combination.readmap)) | 205 if (${yrange} == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { |
206 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}), par.settings=par.settings.readmap)) } | |
204 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size)) | 207 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size)) |
205 plot.list=rbind(read_plot.list, size_plot.list ) | 208 plot.list=rbind(readmap_plot.list, size_plot.list ) |
206 args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1, | 209 args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1, |
207 main=textGrob("${title}", gp=gpar(cex=1), just="top"), | 210 main=textGrob("${title}", gp=gpar(cex=1), just="top"), |
208 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90), | 211 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90), |
209 sub=textGrob("${xlabel}", gp=gpar(cex=1), just="bottom") | 212 sub=textGrob("${xlabel}", gp=gpar(cex=1), just="bottom") |
210 ) | 213 ) |