Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

changeset 20:45df4c72a780 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 521b1e3fcf3dbf9d61d6b2b90d2415c3dadc4b5a
author drosofff
date Wed, 26 Sep 2018 11:06:34 -0400
parents 675033bcb79e
children
files plot_size_readmap.r readmap.xml
diffstat 2 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/plot_size_readmap.r	Wed Dec 20 19:24:55 2017 -0500
+++ b/plot_size_readmap.r	Wed Sep 26 11:06:34 2018 -0400
@@ -99,7 +99,7 @@
 end=i+rows_per_page-1
 if (end>n_genes) {end=n_genes}
 if (args$yrange == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
-readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args.yrange, args.yrange) , par.settings=par.settings.readmap)) }
+readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args$yrange, args$yrange) , par.settings=par.settings.readmap)) }
 args_list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1,
                                     top=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"),
                                     left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90)
@@ -131,7 +131,7 @@
 end=i+rows_per_page/2-1
 if (end>n_genes) {end=n_genes}
 if (args$yrange == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
-readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args.yrange, args.yrange), par.settings=par.settings.readmap)) }
+readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args$yrange, args$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+1, ncol=1,
@@ -142,4 +142,4 @@
             )
 do.call(grid.arrange, args_list)
 }
-devname=dev.off()
\ No newline at end of file
+devname=dev.off()
--- a/readmap.xml	Wed Dec 20 19:24:55 2017 -0500
+++ b/readmap.xml	Wed Sep 26 11:06:34 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.2.7.3">
+<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.2.7.4">
     <description>from sRbowtie aligment</description>
   <requirements>
         <requirement type="package" version="1.1.2=py27_0">bowtie</requirement>
@@ -65,7 +65,7 @@
                 <option value="history">Use one from the history</option>
             </param>
             <when value="indexed">
-                <repeat name="series" title="Add alignment files">
+                <repeat name="series" title="Add alignment files" min="1">
                     <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam">
                         <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
                     </param>
@@ -74,7 +74,7 @@
             </when>
             <when value="history">
                 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" />
-                <repeat name="series" title="Add alignment files">
+                <repeat name="series" title="Add alignment files" min="1">
                     <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/>
                     <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
                 </repeat>