Mercurial > repos > diego > rtg_investigator
comparison tools/rtg/cgsim.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_cgsim" name="Simulate CG reads"> | |
2 <description>with RTG cgsim</description> | |
3 <command interpreter="bash">galaxy-rtg-wrapper.sh cgsim | |
4 -t ${input.extra_files_path} | |
5 #if $limit.sType == "numreads": | |
6 -n $limit.n | |
7 #else | |
8 -c $limit.c | |
9 #end if | |
10 -m $m | |
11 -M $M | |
12 --seed $seed | |
13 -o ${output.extra_files_path} >$output</command> | |
14 <inputs> | |
15 | |
16 <param name="input" type="data" format="rtg_sdf" label="Source SDF"/> | |
17 <param name="m" type="integer" value="350" label="Minimum fragment length" help=""/> | |
18 <param name="M" type="integer" value="500" label="Maximum fragment length" help=""/> | |
19 | |
20 <conditional name="limit"> | |
21 <param name="sType" type="select" label="Select read limit"> | |
22 <option value="numreads">Fixed number of reads</option> | |
23 <option value="coverage">Fixed coverage</option> | |
24 </param> | |
25 <when value="numreads"> | |
26 <param name="n" type="integer" value="1000" label="Number of reads" help="Total number of reads"/> | |
27 </when> | |
28 <when value="coverage"> | |
29 <param name="c" type="float" value="1" label="Coverage" help="Total coverage"/> | |
30 </when> | |
31 </conditional> | |
32 | |
33 <param name="seed" type="integer" label="Seed" value="42" help="Seed for the random number generator"/> | |
34 </inputs> | |
35 <outputs> | |
36 <data format="rtg_sdf" name="output" /> | |
37 </outputs> | |
38 | |
39 <help> | |
40 This tool creates an SDF containing randomly generated CG reads. | |
41 </help> | |
42 | |
43 </tool> |