Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

comparison readmap.xml @ 1:e4874d1ae69d 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 450d1b3d954cc7d96e53652d468811546951f995
author drosofff
date Thu, 26 Nov 2015 11:56:07 -0500
parents ac7d8e55bb67
children ebfc73c72652
comparison
equal deleted inserted replaced
0:ac7d8e55bb67 1:e4874d1ae69d
1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.4"> 1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.5">
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>
155 ## end of function parameters' 155 ## end of function parameters'
156 156
157 ## GRAPHS 157 ## GRAPHS
158 158
159 if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else { 159 if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else {
160 rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 } 160 rows_per_page= 8; page_height_simple = 11.69; page_height_combi=11.69; extrarow=0 }
161 if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test 161 ## 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= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 }
163 if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test
162 164
163 pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width) 165 pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width)
164 for (i in seq(1,n_genes,rows_per_page)) { 166 for (i in seq(1,n_genes,rows_per_page)) {
165 start=i 167 start=i
166 end=i+rows_per_page-1 168 end=i+rows_per_page-1