comparison vcfrandomsample.xml @ 1:03030ecd1961 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 0b9b6512272b82637c2f1e831367e89aed77ae79

0:ad12ba1db0e4

<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>

1:03030ecd1961

<tool id="vcfrandomsample" name="VCFrandomSample:" version="@WRAPPER_VERSION@.0">
    <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="" />
            <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>