Mercurial > repos > anton > vcfrandomsample
comparison vcfrandomsample.xml @ 0:81b9a3179670
Imported from capsule None
| author | anton |
|---|---|
| date | Wed, 11 Jun 2014 17:11:37 -0400 |
| parents | |
| children | a67b14d368a4 |
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| -1:000000000000 | 0:81b9a3179670 |
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| 1 <tool id="vcfrandomsample" name="VCFrandomSample:" version="0.0.1"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement> | |
| 4 </requirements> | |
| 5 <description>Randomly sample sites from VCF dataset</description> | |
| 6 <command> | |
| 7 | |
| 8 #if $adv_options.adv_options_selector == True: | |
| 9 vcfrandomsample -s "${adv_options.scale_by}" -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}" | |
| 10 #else: | |
| 11 vcfrandomsample -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}" | |
| 12 #end if | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param format="vcf" name="vcf_input" type="data" label="Select random sites from"/> | |
| 16 <param name="rate" type="float" value="0.1" label="base sampling probability per locus" help="-r, --rate"/> | |
| 17 <param name="random_seed" type="integer" value="17823618326" label="use this random seed" help="-p, --random-seed; use this to make results reproducible" /> | |
| 18 <conditional name="adv_options"> | |
| 19 <param name="adv_options_selector" type="boolean" truevalue="use_adv_controls" label="Advanced controls" help="Allows you to specify options that are not listed above"/> | |
| 20 <when value="use_adv_controls"> | |
| 21 <param name="scale_by" type="text" value="AF" label="scale sampling likelihood by this INFO field" help="-s, --scale-by; this only works for Float info fields such as AF" /> | |
| 22 </when> | |
| 23 </conditional> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format="vcf" name="out_file1" /> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="vcf_input" value="vcflib.vcf"/> | |
| 31 <param name="rate" value="0.2" /> | |
| 32 <param name="random_seed" value="1" /> | |
| 33 <param name="adv_options_selector" value="False" /> | |
| 34 <output name="out_file1" file="vcfrandomsample-test1.vcf" lines_diff="2" /> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 | |
| 39 Randomly sample sites from an input VCF file. Scale the sampling probability by the field specified by --scale-by (see advanced controls). This may be | |
| 40 used to provide uniform sampling across allele frequencies, for instance (AF field in this case). | |
| 41 | |
| 42 Options:: | |
| 43 | |
| 44 -r, --rate RATE base sampling probability per locus | |
| 45 -s, --scale-by KEY scale sampling likelihood by this Float info field | |
| 46 -p, --random-seed N use this random seed | |
| 47 | |
| 48 ---- | |
| 49 | |
| 50 Vcfrandomsample is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 51 | |
| 52 </help> | |
| 53 </tool> |