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comparison tools/rtg/readsim.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_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>