Mercurial > repos > jjjjia > cpo_prediction

comparison cpo_snippy.xml @ 5:698579246d0d draft

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planemo upload
author jjjjia
date Tue, 21 Aug 2018 17:53:08 -0400
parents fea89c4d5227
children 4b2738bc81ed
comparison
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4:bd6f5844d60e 5:698579246d0d
1 <tool id="snippy" name="snippy" version="3.2"> 1 <tool id="cpo_snippy" name="CPO_Snippy" version="3.2">
2 <description>Modified Snippy v3.2 to support contig inputs for the cpo_prediction workflow</description>
2 <requirements> 3 <requirements>
3 <requirement type="package" version="3.2">snippy</requirement> 4 <requirement type="package" version="3.2">snippy</requirement>
4 </requirements> 5 </requirements>
5 <stdio> 6 <stdio>
6 <exit_code range="1:" /> 7 <exit_code range="1:" />
30 31
31 gunzip out/snps.depth.gz 32 gunzip out/snps.depth.gz
32 33
33 && 34 &&
34 35
35 tar -czf out.tgz out 36 #import re
37 #set $dir_name = re.sub('[^\w_]', '_', $input.element_identifier)
38 mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&
39
40 tar -czf out.tgz ${dir_name}
36 41
37 42
38 ]]> 43 ]]>
39 </command> 44 </command>
40 <inputs> 45 <inputs>