Mercurial > repos > diego > rtg_investigator
comparison tools/rtg/cgmap.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_cgmap" name="CG map"> | |
2 <description>reads with rtg cg map</description> | |
3 <command interpreter="bash">galaxy-rtg-map-wrapper.sh paired $output1 $output2 $__new_file_path__ | |
4 cgmap -t ${template.extra_files_path} | |
5 --repeat-freq ${repeat} | |
6 -i ${reads.extra_files_path} | |
7 --min-insert-size $minlength --max-insert-size $maxlength | |
8 --max-mated-score $maxscore --max-unmated-score $maxuscore | |
9 </command> | |
10 <inputs> | |
11 <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/> | |
12 <param name="reads" type="data" format="rtg_sdf" label="Reads SDF"/> | |
13 <param name="repeat" type="text" value="90%" label="Repeat frequency"> | |
14 <sanitizer sanitize="False"/> | |
15 </param> | |
16 | |
17 <param name="maxscore" type="text" value="10%" label="Maximum alignment score for mated reads"> | |
18 <sanitizer sanitize="False"/> | |
19 </param> | |
20 <param name="maxuscore" type="text" value="10%" label="Maximum alignment score for umated reads"> | |
21 <sanitizer sanitize="False"/> | |
22 </param> | |
23 <param name="minlength" type="integer" value="0" label="Minimum insert size"/> | |
24 <param name="maxlength" type="integer" value="1000" label="Maximum insert size"/> | |
25 | |
26 </inputs> | |
27 <outputs> | |
28 <data name="output1" format="samix" label="Cgmap mated on reads data ${reads.hid} and template data ${template.hid}"/> | |
29 <data name="output2" format="samix" label="Cgmap unmated on reads data ${reads.hid} and template data ${template.hid}"/> | |
30 </outputs> | |
31 | |
32 <help> | |
33 This tool performs a NGS read mapping using rtg cgmap | |
34 </help> | |
35 | |
36 </tool> |