Mercurial > repos > wolma > mimodd
comparison reheader.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 |
|---|---|
| 1 <tool id="reheader" name="Reheader BAM file" version="0.1.7.2"> | 1 <tool id="reheader" name="Reheader BAM file" version="0.1.7.2"> |
| 2 <description>From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file</description> | 2 <description>From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file</description> |
| 3 <expand macro="requirements"/> | 3 <expand macro="requirements"/> |
| 4 <version_command>mimodd version -q</version_command> | 4 <version_command>python3 -m MiModD version -q</version_command> |
| 5 <command> | 5 <command> |
| 6 #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore": | 6 #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore": |
| 7 mimodd header | 7 python3 -m MiModD header |
| 8 #if $str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form": | 8 #if $str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form": |
| 9 #for $rginfo in $rg.rginfo.rg | 9 #for $rginfo in $rg.rginfo.rg |
| 10 #if $str($rginfo.source_id): | 10 #if $str($rginfo.source_id): |
| 11 --rg-id "${rginfo.source_id}" | 11 --rg-id "${rginfo.source_id}" |
| 12 #end if | 12 #end if |
| 58 #end if | 58 #end if |
| 59 #end for | 59 #end for |
| 60 #end if | 60 #end if |
| 61 | | 61 | |
| 62 #end if | 62 #end if |
| 63 mimodd reheader "$inputfile" --sq ignore | 63 python3 -m MiModD reheader "$inputfile" --sq ignore |
| 64 --rg ${rg.treat_rg} | 64 --rg ${rg.treat_rg} |
| 65 #if $str($rg.treat_rg) != "ignore": | 65 #if $str($rg.treat_rg) != "ignore": |
| 66 #if $str($rg.rginfo.source) == "from_file": | 66 #if $str($rg.rginfo.source) == "from_file": |
| 67 "${rg.rginfo.data}" | 67 "${rg.rginfo.data}" |
| 68 #else: | 68 #else: |