Mercurial > repos > wolma > mimodd

comparison reheader.xml @ 3:ba685c655e18

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author wolma
date Wed, 11 Feb 2015 09:26:43 -0500
parents 72d20758ba2c
children bdd1995c9e66
comparison
equal deleted inserted replaced
2:72d20758ba2c 3:ba685c655e18
1 <tool id="reheader" name="Reheader BAM file"> 1 <tool id="reheader" name="Reheader BAM file">
2 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> 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>
4 <macros>
5 <import>toolshed_macros.xml</import>
6 </macros>
7 <expand macro="requirements"/> 4 <expand macro="requirements"/>
8 <version_command>mimodd version -q</version_command> 5 <version_command>mimodd version -q</version_command>
9 <command> 6 <command>
10 #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore": 7 #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore":
11 mimodd header 8 mimodd header
102 99
103 -o "$output" 100 -o "$output"
104 </command> 101 </command>
105 102
106 <macros> 103 <macros>
104 <import>toolshed_macros.xml</import>
107 <macro name="getreadgroupinfo"> 105 <macro name="getreadgroupinfo">
108 <conditional name="rginfo"> 106 <conditional name="rginfo">
109 <param name="source" type="select" label="source of new read-group information" help=""> 107 <param name="source" type="select" label="source of new read-group information" help="">
110 <option value="from_file">existing SAM file</option> 108 <option value="from_file">existing SAM file</option>
111 <option value="from_form">input form</option> 109 <option value="from_form">input form</option>