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comparison tools/rtg/cgmap.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_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>