diff 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

--- a/readmap.xml	Thu Nov 26 11:56:07 2015 -0500
+++ b/readmap.xml	Wed Feb 03 09:20:34 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.5">
+<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.2">
   <description>from sRbowtie aligment</description>
   <requirements>
         <requirement type="package" version="0.12.7">bowtie</requirement>
@@ -78,6 +78,7 @@
                 <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/>
                 <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/>
                 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/>
+                <param name="yrange" type="integer" size="3" value="0" label="y axis range for readmaps. 0 means auto-scaling."/>
                 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?">
 		  <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/>
                 </param>
@@ -167,7 +168,8 @@
         start=i
         end=i+rows_per_page-1
         if (end>n_genes) {end=n_genes}
-        readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap))
+        if (${yrange} == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
+        readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}) , par.settings=par.settings.readmap)) }
         args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1,
                                             main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"),
                                             left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
@@ -200,9 +202,10 @@
         start=i
         end=i+rows_per_page/2-1
         if (end>n_genes) {end=n_genes}
-	read_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.combination.readmap))
+        if (${yrange} == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
+        readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}), par.settings=par.settings.readmap)) }
         size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
-	plot.list=rbind(read_plot.list, size_plot.list )
+	plot.list=rbind(readmap_plot.list, size_plot.list )
         args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1,
                                     main=textGrob("${title}", gp=gpar(cex=1), just="top"),
                                     left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90),