Mercurial > repos > wolma > mimodd
comparison snap_caller.xml @ 21:c46406466625 draft
Uploaded
author | wolma |
---|---|
date | Sat, 11 Jun 2016 19:10:44 -0400 |
parents | 93db2f9bca12 |
children | 5db0545b9004 |
comparison
equal
deleted
inserted
replaced
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"): |