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

1:e4874d1ae69d

<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.5">
  <description>from sRbowtie aligment</description>
  <requirements>
        <requirement type="package" version="0.12.7">bowtie</requirement>
        <requirement type="package" version="0.7.7">pysam</requirement>
        <requirement type="package" version="3.1.2">R</requirement>

                <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/>
                <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/>
                <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="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>
  </inputs>
   <configfiles>

      pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width)
      for (i in seq(1,n_genes,rows_per_page)) {
        start=i
        end=i+rows_per_page-1
        if (end>n_genes) {end=n_genes}
        readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap))
        args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1,
                                            main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"),
                                            left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
                                            #sub=textGrob("readmap coordinates", gp=gpar(cex=.75), just="bottom")
                                            )

      pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width)
      for (i in seq(1,n_genes,rows_per_page/2)) {
        start=i
        end=i+rows_per_page/2-1
        if (end>n_genes) {end=n_genes}
	read_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.combination.readmap))
        size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
	plot.list=rbind(read_plot.list, size_plot.list )
        args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1,
                                    main=textGrob("${title}", gp=gpar(cex=1), just="top"),
                                    left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90),
                                    sub=textGrob("${xlabel}", gp=gpar(cex=1), just="bottom")
                                    )

2:ebfc73c72652

<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>
        <requirement type="package" version="0.7.7">pysam</requirement>
        <requirement type="package" version="3.1.2">R</requirement>

                <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/>
                <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/>
                <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>
  </inputs>
   <configfiles>

      pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width)
      for (i in seq(1,n_genes,rows_per_page)) {
        start=i
        end=i+rows_per_page-1
        if (end>n_genes) {end=n_genes}
        if (${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)
                                            #sub=textGrob("readmap coordinates", gp=gpar(cex=.75), just="bottom")
                                            )

      pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width)
      for (i in seq(1,n_genes,rows_per_page/2)) {
        start=i
        end=i+rows_per_page/2-1
        if (end>n_genes) {end=n_genes}
        if (${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}, ${yrange}), par.settings=par.settings.readmap)) }
        size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
	plot.list=rbind(readmap_plot.list, size_plot.list )
        args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1,
                                    main=textGrob("${title}", gp=gpar(cex=1), just="top"),
                                    left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90),
                                    sub=textGrob("${xlabel}", gp=gpar(cex=1), just="bottom")
                                    )