Mercurial > repos > diego > rtg_investigator
comparison tools/rtg/snpsim.xml @ 1:8593828f91e7 default tip
Full galaxy wrapper
| author | diego |
|---|---|
| date | Sat, 21 Apr 2012 21:36:15 -0400 |
| parents | |
| children |
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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> |