comparison shapeit_phase.xml @ 19:42bafd3c5a83 draft

planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 75ae96395b13aafb20f82b220c4d14ac484b6767-dirty

18:d3515c2a3f51

<tool id="shapeit_phase" name="shapeit_phase" version="0.17.0">
    <description>genomic data with or without reference panel</description>
    <requirements>
        <requirement type="package" version="2.r837">shapeit</requirement>
    </requirements>
    <stdio>

          #if $use_filters.filter_individuals == "exclude_individuals":
            --exclude-ind $use_filters.exclude_inviduals_file
          #else if $use_filters.filter_individuals == "include_individuals":
            --include-ind $use_filters.include_inviduals_file
          #end if
          #if $use_filters.filter_individuals == "exclude_SNPs":
            --exclude-snp $use_filters.exclude_SNPs_file
          #else if $use_filters.filter_SNPs == "include_SNPs":
            --include-snp $use_filters.include_SNPs_file
          #end if
        #end if

        #if $use_advanced_parameters.use_advanced_parameters_select == "use_advanced_parameters_yes":
          #if $use_advanced_parameters.chrX == "chrX_yes":
            --chrX
          #end if
          #if $use_advanced_parameters.noped == "noped_yes":
            --noped

          <option value="use_advanced_parameters_yes">Use advanced parameters</option>
          <option value="use_advanced_parameters_no" selected="True">Use standard parameters</option>
        </param>

        <when value="use_advanced_parameters_yes">
          <param name="chrX" type="select" label="Use X chromosomal genotypes?">
            <option value="chrX_yes">Yes</option>
            <option value="chrX_no" selected="True">No</option>
          </param>

            </when>
          </conditional>

          <conditional name="filter_SNPs">
            <param name="filter_SNPs_select" type="select" label="Do you want to filter SNPs?">
              <option value="no_individual_filter" selected="True">No filtering</option>
              <option value="exclude_SNPs">Exclude list of SNPs</option>
              <option value="include_SNPs">Limit list of SNPs</option>
            </param>
            <when value="no_individual_filter"></when>
            <when value="exclude_SNPs">
              <param name="exclude_inviduals_file" type="data" format="txt" label="Specify file with excluded SNPs (.exc)"/>
            </when>
            <when value="include_SNPs">
              <param name="include_inviduals_file" type="data" format="txt" label="Specify file with limited SNPs (.inc)"/>
            </when>
          </conditional>
        </when>
        <when value="use_filters_no"></when>
      </conditional>

19:42bafd3c5a83

<tool id="shapeit_phase" name="shapeit_phase" version="0.18.0">
    <description>genomic data with or without reference panel</description>
    <requirements>
        <requirement type="package" version="2.r837">shapeit</requirement>
    </requirements>
    <stdio>

          #if $use_filters.filter_individuals == "exclude_individuals":
            --exclude-ind $use_filters.exclude_inviduals_file
          #else if $use_filters.filter_individuals == "include_individuals":
            --include-ind $use_filters.include_inviduals_file
          #end if
          #if $use_filters.filter_SNPs.filter_SNPs_select == "exclude_SNPs":
            --exclude-snp $use_filters.filter_SNPs.exclude_SNPs_file
          #else if $use_filters.filter_SNPs.filter_SNPs_select  == "include_SNPs":
            --include-snp $use_filters.filter_SNPs.include_SNPs_file
          #end if
        #end if

        #if $use_advanced_parameters.use_advanced_parameters_select == "use_advanced_parameters_yes":
          $use_advanced_parameters.duohmm
          #if $use_advanced_parameters.chrX == "chrX_yes":
            --chrX
          #end if
          #if $use_advanced_parameters.noped == "noped_yes":
            --noped

          <option value="use_advanced_parameters_yes">Use advanced parameters</option>
          <option value="use_advanced_parameters_no" selected="True">Use standard parameters</option>
        </param>

        <when value="use_advanced_parameters_yes">
          <param argument="--duohmm" type="boolean" truevalue="--duohmm" falsevalue="" />
          <param name="chrX" type="select" label="Use X chromosomal genotypes?">
            <option value="chrX_yes">Yes</option>
            <option value="chrX_no" selected="True">No</option>
          </param>

            </when>
          </conditional>

          <conditional name="filter_SNPs">
            <param name="filter_SNPs_select" type="select" label="Do you want to filter SNPs?">
              <option value="no_SNPs_filter" selected="True">No filtering</option>
              <option value="exclude_SNPs">Exclude list of SNPs</option>
              <option value="include_SNPs">Limit list of SNPs</option>
            </param>
            <when value="no_individual_filter"></when>
            <when value="exclude_SNPs">
              <param name="exclude_SNPs_file" type="data" format="txt" label="Specify file with excluded SNPs (.exc)"/>
            </when>
            <when value="include_SNPs">
              <param name="include_SNPs_file" type="data" format="txt" label="Specify file with limited SNPs (.inc)"/>
            </when>
          </conditional>
        </when>
        <when value="use_filters_no"></when>
      </conditional>