Mercurial > repos > wolma > mimodd
comparison deletion_predictor.xml @ 21:c46406466625 draft
Uploaded
| 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 |