Mercurial > repos > devteam > vcfrandomsample
view vcfrandomsample.xml @ 3:f7e6495859b9 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample commit 36e9065027cc7bf721e9d203208477ee88906c57"
author | iuc |
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date | Thu, 23 Jan 2020 12:58:59 +0000 |
parents | 939834d8de40 |
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<tool id="vcfrandomsample" name="VCFrandomSample:" version="@WRAPPER_VERSION@+galaxy0"> <description>Randomly sample sites from VCF dataset</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio" /> <command> vcfrandomsample #if $adv_options.adv_options_selector == "use_adv_controls": -s '${adv_options.scale_by}' #end if -p ${random_seed} -r ${rate} '${vcf_input}' > '${out_file1}' </command> <inputs> <param format="vcf" name="vcf_input" type="data" label="Select random sites from"/> <param name="rate" type="float" value="0.1" label="base sampling probability per locus" help="-r, --rate"/> <param name="random_seed" type="integer" value="17823618326" label="use this random seed" help="-p, --random-seed; use this to make results reproducible" /> <conditional name="adv_options"> <param name="adv_options_selector" type="select" label="Advanced controls" help="Allows you to specify options that are not listed above"> <option value="no">Don't use advanced options</option> <option value="use_adv_controls">Use advanced options</option> </param> <when value="no" /> <when value="use_adv_controls"> <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" /> </when> </conditional> </inputs> <outputs> <data format="vcf" name="out_file1" /> </outputs> <tests> <test> <param name="vcf_input" value="vcflib.vcf"/> <param name="rate" value="0.2" /> <param name="random_seed" value="1" /> <param name="adv_options_selector" value="no" /> <output name="out_file1" file="vcfrandomsample-test1.vcf" lines_diff="2" /> </test> </tests> <help> Randomly sample sites from an input VCF dataset. Scale the sampling probability by the field specified by --scale-by (see advanced controls). This may be used to provide uniform sampling across allele frequencies, for instance (AF field in this case). ---- Vcfrandomsample @IS_PART_OF_VCFLIB@ </help> <expand macro="citations" /> </tool>