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comparison tools/rtg/cgsim.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_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>