Mercurial > repos > diego > rtg_investigator
comparison tools/rtg/map.xml @ 1:8593828f91e7 default tip
Full galaxy wrapper
author | diego |
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date | Sat, 21 Apr 2012 21:36:15 -0400 |
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0:d50638ebd809 | 1:8593828f91e7 |
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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> |