comparison deletion_predictor.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>Predicts deletions in one or more aligned read samples based on coverage of the reference genome and on insert sizes</description> 2 <description>Predicts deletions in one or more aligned read samples based on coverage of the reference genome and on insert sizes</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 delcall 9 python3 -m MiModD delcall
10 #for $l in $list_input 10 #for $l in $list_input
11 "${l.bamfile}" 11 "${l.bamfile}"
12 #end for 12 #end for
13 "$covfile" -o "$outputfile" 13 "$covfile" -o "$outputfile"
14 --max-cov "$max_cov" --min-size "$min_size" $include_uncovered $group_by_id --verbose 14 --max-cov "$max_cov" --min-size "$min_size" $include_uncovered $group_by_id --verbose