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comparison tools/rtg/map.xml @ 1:8593828f91e7 default tip

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Full galaxy wrapper
author diego
date Sat, 21 Apr 2012 21:36:15 -0400
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0:d50638ebd809 1:8593828f91e7
1 <tool id="rtg_map" name="Map">
2 <description>reads with rtg map</description>
3 <command interpreter="bash">galaxy-rtg-map-wrapper.sh $paired.sPaired $output1 $output2 $__new_file_path__
4 map -t ${template.extra_files_path}
5 --repeat-freq ${repeat}
6 -i ${reads.extra_files_path}
7 #if $paired.sPaired == "paired":
8 --min-insert-size $paired.minlength --max-insert-size $paired.maxlength
9 --max-mated-score $paired.maxscore --max-unmated-score $paired.maxuscore
10 #else:
11 --max-alignment-score $paired.maxscore
12 #end if
13 </command>
14 <inputs>
15 <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
16 <param name="reads" type="data" format="rtg_sdf" label="Reads SDF"/>
17 <param name="repeat" type="text" value="90%" label="Repeat frequency">
18 <sanitizer sanitize="False"/>
19 </param>
20
21 <conditional name="paired">
22 <param name="sPaired" type="select" label="Are you mapping paired-end reads?">
23 <option value="paired">Paired-end</option>
24 <option value="single">Single-end</option>
25 </param>
26 <when value="single">
27 <param name="maxscore" type="text" value="10%" label="Maximum alignment score for reads (percentages do not work ATM)">
28 <sanitizer sanitize="False"/>
29 </param>
30 </when>
31 <when value="paired">
32 <param name="maxscore" type="text" value="10%" label="Maximum alignment score for mated reads">
33 <sanitizer sanitize="False"/>
34 </param>
35 <param name="maxuscore" type="text" value="10%" label="Maximum alignment score for umated reads">
36 <sanitizer sanitize="False"/>
37 </param>
38 <param name="minlength" type="integer" value="200" label="Minimum insert size"/>
39 <param name="maxlength" type="integer" value="400" label="Maximum insert size"/>
40 </when>
41 </conditional>
42
43 </inputs>
44 <outputs>
45 <data name="output1" format="samix" />
46 <data name="output2" format="samix" >
47 <filter>paired['sPaired'] == "paired"</filter>
48 </data>
49 </outputs>
50
51 <help>
52 This tool performs a NGS read mapping using rtg map
53 </help>
54
55 </tool>