| Previous changeset 19:675033bcb79e (2017-12-20) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 521b1e3fcf3dbf9d61d6b2b90d2415c3dadc4b5a |
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modified:
plot_size_readmap.r readmap.xml |
| b |
| diff -r 675033bcb79e -r 45df4c72a780 plot_size_readmap.r --- 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() |
| b |
| diff -r 675033bcb79e -r 45df4c72a780 readmap.xml --- a/readmap.xml Wed Dec 20 19:24:55 2017 -0500 +++ b/readmap.xml Wed Sep 26 11:06:34 2018 -0400 |
| b |
| @@ -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> |