Mercurial > repos > diego > rtg_investigator
comparison tools/rtg/snpsim.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_snpsim" name="Simulate SNPs"> | |
2 <description>with rtg snpsim</description> | |
3 <command interpreter="bash">galaxy-rtg-snpsim-wrapper.sh ${output3} ${output3.extra_files_path} snpsim | |
4 --seed $seed -i ${input.extra_files_path} | |
5 -o ${output.extra_files_path} | |
6 #if $str($diploid) == "true": | |
7 -O ${output2.extra_files_path} | |
8 #end if | |
9 >$output</command> | |
10 <inputs> | |
11 <param name="input" type="data" format="rtg_sdf" label="SDF containing input genome"/> | |
12 <param name="diploid" type="select" label="Generate diploid mutations"> | |
13 <option value="true">Yes</option> | |
14 <option value="false" selected="true">No</option> | |
15 </param> | |
16 <param name="seed" type="integer" value="42" label="Seed" help="Seed for the random number generator"/> | |
17 </inputs> | |
18 <outputs> | |
19 <data format="rtg_sdf" name="output" label="Mutated genome on data ${input.hid}"/> | |
20 <data format="rtg_sdf" name="output2" label="Second mutated genome on data ${input.hid}"> | |
21 <filter>diploid == "true"</filter> | |
22 </data> | |
23 <data format="vcf" name="output3" label="SNPs file generated on data ${input.hid}" /> | |
24 </outputs> | |
25 | |
26 <help> | |
27 This tool creates a simulated mutation of a reference genome. Can generate either haploid or diploid mutations. | |
28 </help> | |
29 | |
30 </tool> |