Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
comparison readmap.xml @ 6:68f58363f1c6 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 78fca5d46c4554514bc51b0010a7611aaced40b9-dirty
author | drosofff |
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date | Thu, 04 Feb 2016 08:41:48 -0500 |
parents | 4efe210c91f3 |
children | be0c6b6466cc |
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5:bcc0c7093e7a | 6:68f58363f1c6 |
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1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.3"> | 1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.5"> |
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> |
156 ## end of function parameters' | 156 ## end of function parameters' |
157 | 157 |
158 ## GRAPHS | 158 ## GRAPHS |
159 | 159 |
160 if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else { | 160 if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else { |
161 rows_per_page= 8; page_height_simple = 11.69; page_height_combi=11.69; extrarow=0 } | 161 rows_per_page= n_genes; page_height_simple = 2.5*n_genes; page_height_combi=page_height_simple*2; extrarow=0 } |
162 ## rows_per_page= 8; page_height_simple = 11.69/7*n_genes; page_height_combi=11.69/9*(n_genes*2); extrarow=0 } | 162 ## rows_per_page= 8; page_height_simple = 11.69/7*n_genes; page_height_combi=11.69/9*(n_genes*2); extrarow=0 } |
163 ## rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 } | 163 ## rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 } |
164 if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test | 164 if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test |
165 | 165 |
166 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) |
196 do.call(grid.arrange, args.list) | 196 do.call(grid.arrange, args.list) |
197 } | 197 } |
198 devname=dev.off() | 198 devname=dev.off() |
199 | 199 |
200 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) |
201 if (rows_per_page %% 2 != 0) { rows_per_page = rows_per_page + 1} | |
201 for (i in seq(1,n_genes,rows_per_page/2)) { | 202 for (i in seq(1,n_genes,rows_per_page/2)) { |
202 start=i | 203 start=i |
203 end=i+rows_per_page/2-1 | 204 end=i+rows_per_page/2-1 |
204 if (end>n_genes) {end=n_genes} | 205 if (end>n_genes) {end=n_genes} |
205 if (${yrange} == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { | 206 if (${yrange} == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { |