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comparison readmap.xml @ 6:68f58363f1c6 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 78fca5d46c4554514bc51b0010a7611aaced40b9-dirty
author drosofff
date Thu, 04 Feb 2016 08:41:48 -0500
parents 4efe210c91f3
children be0c6b6466cc
comparison
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5:bcc0c7093e7a 6:68f58363f1c6
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 {