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comparison reheader.xml @ 5:bdd1995c9e66

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upgrade to mimodd version 0.1.6.1
author Wolfgang Maier
date Tue, 28 Jul 2015 23:21:11 +0200
parents ba685c655e18
children 85214e4428fd
comparison
equal deleted inserted replaced
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