<tool id="vcfrandomsample" name="VCFrandomSample:" version="0.0.3">
  <description>Randomly sample sites from VCF dataset</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio" />
  <command>

    #if $adv_options.adv_options_selector == True:
        vcfrandomsample -s "${adv_options.scale_by}" -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}"
    #else:
        vcfrandomsample -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}" 
    #end if                                                                      
  </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="boolean" truevalue="use_adv_controls" label="Advanced controls" help="Allows you to specify options that are not listed above"/>
      <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="False" />
      <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).

Options::

    -r, --rate RATE      base sampling probability per locus
    -s, --scale-by KEY   scale sampling likelihood by this Float info field
    -p, --random-seed N  use this random seed

----

Vcfrandomsample @IS_PART_OF_VCFLIB@
</help>
  <expand macro="citations" />
</tool>