Mercurial > repos > iuc > cnvkit_autobin

comparison autobin.xml @ 1:94e1d19c8190 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:42:07 +0000
parents fff49e30af46
children
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0:fff49e30af46 1:94e1d19c8190
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="creators"/>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 #import re 10 #import re
10 #set $names = [] 11 #set $names = []
11 #set $x=1 12 #set $x=1
12 #for $x, $bam in enumerate($bams): 13 #for $x, $bam in enumerate($bams):
13 #set $name_base = re.sub('[^\w\-_\.]', '_', $bam.element_identifier) 14 #set $name_base = re.sub('[^\w\-_\.]', '_', $bam.element_identifier)
14 #set $name = $name_base + '_' + str(x) 15 #set $name = $name_base
15 #silent $names.append( $name ) 16 #silent $names.append( $name )
16 ln -s '$bam' ${name}.bam && 17 ln -s '$bam' ${name}.bam &&
17 ln -s '${bam.metadata.bam_index}' ${name}.bai && 18 ln -s '${bam.metadata.bam_index}' ${name}.bai &&
18 #end for 19 #end for
19 ln -s '$targets' ./capture.bed && 20 ln -s '$targets' ./capture.bed &&