Mercurial > repos > nilesh > rseqc

comparison geneBody_coverage.xml @ 46:68ada7ca4cc4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fixed geneBody coverage sample names
author lparsons
date Mon, 29 Sep 2014 16:32:13 -0400
parents eb339c5849bb
children
comparison
equal deleted inserted replaced
45:eb339c5849bb 46:68ada7ca4cc4
7 <requirement type="package" version="1.7.1">numpy</requirement> 7 <requirement type="package" version="1.7.1">numpy</requirement>
8 <requirement type="package" version="2.4">rseqc</requirement> 8 <requirement type="package" version="2.4">rseqc</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $input.display_name) 11 #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $input.display_name)
12 #set $fname = "dataset_1_" + str($safename) + ".bam" 12 #set $fname = "d1_" + str($safename) + ".bam"
13 ln -s '${input}' '${fname}' &amp;&amp; 13 ln -s '${input}' '${fname}' &amp;&amp;
14 ln -s '${input.metadata.bam_index}' '${fname}.bai' &amp;&amp; 14 ln -s '${input.metadata.bam_index}' '${fname}.bai' &amp;&amp;
15 echo '${fname}' > input_list.txt &amp;&amp; 15 echo '${fname}' > input_list.txt &amp;&amp;
16 #for $i, $additional_input in enumerate($additionalinputs): 16 #for $i, $additional_input in enumerate($additionalinputs):
17 #set $index = $i+2 17 #set $index = $i+2
18 #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $input.display_name) 18 #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $additional_input.file.display_name)
19 #set $fname = 'dataset_' + str($index) + '_' + str($safename) + ".bam" 19 #set $fname = 'd' + str($index) + '_' + str($safename) + ".bam"
20 ln -s '$additional_input.file' '${fname}' &amp;&amp; 20 ln -s '$additional_input.file' '${fname}' &amp;&amp;
21 ln -s '$additional_input.file.metadata.bam_index' '${fname}.bai' &amp;&amp; 21 ln -s '$additional_input.file.metadata.bam_index' '${fname}.bai' &amp;&amp;
22 echo '${fname}' >> input_list.txt &amp;&amp; 22 echo '${fname}' >> input_list.txt &amp;&amp;
23 #end for 23 #end for
24 geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output 24 geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output