Mercurial > repos > wolma > mimodd
comparison reheader.xml @ 5:bdd1995c9e66
upgrade to mimodd version 0.1.6.1
| author | Wolfgang Maier |
|---|---|
| date | Tue, 28 Jul 2015 23:21:11 +0200 |
| parents | ba685c655e18 |
| children | 85214e4428fd |
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| 4:ffee8534a5c4 | 5:bdd1995c9e66 |
|---|---|
| 1 <tool id="reheader" name="Reheader BAM file"> | 1 <tool id="reheader" name="Reheader BAM file" version="0.1.6.1"> |
| 2 | |
| 3 <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> |
| 4 <expand macro="requirements"/> | 3 <expand macro="requirements"/> |
| 5 <version_command>mimodd version -q</version_command> | 4 <version_command>mimodd version -q</version_command> |
| 6 <command> | 5 <command> |
| 7 #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": |
| 81 - | 80 - |
| 82 #end if | 81 #end if |
| 83 | 82 |
| 84 #set $restr = "" | 83 #set $restr = "" |
| 85 #for $rename in $rg_renaming | 84 #for $rename in $rg_renaming |
| 86 #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '"') | 85 #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '" ') |
| 87 #end for | 86 #end for |
| 88 #if $restr | 87 #if $restr |
| 89 --rgm $restr | 88 --rgm $restr |
| 90 #end if | 89 #end if |
| 91 | 90 |
| 92 #set $restr = "" | 91 #set $restr = "" |
| 93 #for $rename in $sq_renaming | 92 #for $rename in $sq_renaming |
| 94 #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '"') | 93 #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '" ') |
| 95 #end for | 94 #end for |
| 96 #if $restr | 95 #if $restr |
| 97 --sqm $restr | 96 --sqm $restr |
| 98 #end if | 97 #end if |
| 99 | 98 |