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comparison snap_caller.xml @ 21:c46406466625 draft

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author wolma
date Sat, 11 Jun 2016 19:10:44 -0400
parents 93db2f9bca12
children 5db0545b9004
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20:aba6d9b1c1f1 21:c46406466625
2 <description>Map sequence reads to a reference genome using SNAP</description> 2 <description>Map sequence reads to a reference genome using SNAP</description>
3 <macros> 3 <macros>
4 <import>toolshed_macros.xml</import> 4 <import>toolshed_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>mimodd version -q</version_command> 7 <version_command>python3 -m MiModD version -q</version_command>
8 <command> 8 <command>
9 mimodd snap-batch -s 9 python3 -m MiModD snap-batch -s
10 ## SNAP calls (considering different cases) 10 ## SNAP calls (considering different cases)
11 11
12 #for $i in $datasets 12 #for $i in $datasets
13 "snap ${i.mode_choose.mode} '$ref_genome' 13 "snap ${i.mode_choose.mode} '$ref_genome'
14 #if $str($i.mode_choose.mode) == "paired" and $str($i.mode_choose.input.iformat) in ("fastq", "gz"): 14 #if $str($i.mode_choose.mode) == "paired" and $str($i.mode_choose.input.iformat) in ("fastq", "gz"):