Mercurial > repos > diego > rtg_investigator
comparison tools/rtg/readsim.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_readsim" name="Simulate reads"> | |
2 <description>with RTG readsim</description> | |
3 <command interpreter="bash">galaxy-rtg-wrapper.sh readsim | |
4 -t ${input.extra_files_path} | |
5 #if str($input2) != "None": | |
6 -T ${input2.extra_files_path} | |
7 #end if | |
8 #if $limit.sType == "numreads": | |
9 -n $limit.n | |
10 #else | |
11 -c $limit.c | |
12 #end if | |
13 -m $m | |
14 -M $M | |
15 --machine $machine.sMachine | |
16 #if $machine.sMachine == "illumina_se": | |
17 -r $machine.r | |
18 #else if $machine.sMachine == "illumina_pe": | |
19 -L $machine.L | |
20 -R $machine.R | |
21 #else if $machine.sMachine == "454_pe": | |
22 --454-min-total-size $machine.454-min | |
23 --454-max-total-size $machine.454-max | |
24 #end if | |
25 --seed $seed | |
26 -o ${output.extra_files_path} >$output</command> | |
27 <inputs> | |
28 | |
29 <param name="input" type="data" format="rtg_sdf" label="SDF containing input genome"/> | |
30 <param name="input2" type="data" format="rtg_sdf" label="SDF with second genome for simulating diploid genomes" optional="true" /> | |
31 <param name="m" type="integer" value="200" label="Minimum fragment length" help="Total number of reads"/> | |
32 <param name="M" type="integer" value="400" label="Minimum fragment length" help="Total number of reads"/> | |
33 | |
34 <conditional name="limit"> | |
35 <param name="sType" type="select" label="Select read limit"> | |
36 <option value="numreads">Fixed number of reads</option> | |
37 <option value="coverage">Fixed coverage</option> | |
38 </param> | |
39 <when value="numreads"> | |
40 <param name="n" type="integer" value="1000" label="Number of reads" help="Total number of reads"/> | |
41 </when> | |
42 <when value="coverage"> | |
43 <param name="c" type="float" value="1" label="Coverage" help="Total coverage"/> | |
44 </when> | |
45 </conditional> | |
46 | |
47 <conditional name="machine"> | |
48 <param name="sMachine" type="select" label="Select machine type"> | |
49 <option value="illumina_pe">Illumina paired-end</option> | |
50 <option value="illumina_se">Illumina single-end</option> | |
51 <option value="454_pe">454 paired-end</option> | |
52 </param> | |
53 <when value="illumina_se"> | |
54 <param name="r" type="integer" value="100" label="Read length" help="Target read length on left side"/> | |
55 </when> | |
56 <when value="illumina_pe"> | |
57 <param name="L" type="integer" value="100" label="Left read length" help="Target read length on left side"/> | |
58 <param name="R" type="integer" value="100" label="Right read length" help="Target read length on right side"/> | |
59 </when> | |
60 <when value="454_pe"> | |
61 <param name="454-min" type="integer" value="500" label="Minimum total length" help="Minimum sum of left and right read lengths"/> | |
62 <param name="454-max" type="integer" value="300" label="Maximum total length" help="Maximum sum of left and right read lengths"/> | |
63 </when> | |
64 </conditional> | |
65 <param name="seed" type="integer" value="42" label="Seed" help="Seed for the random number generator"/> | |
66 </inputs> | |
67 <outputs> | |
68 <data format="rtg_sdf" name="output" /> | |
69 </outputs> | |
70 | |
71 <help> | |
72 This tool creates an SDF containing randomly generated reads. | |
73 </help> | |
74 | |
75 </tool> |