annotate vcf_phase.xml @ 1:15245deda141 draft

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<tool id="vcf_phase" name="Phase VCF" version="1.0.0.1">

  <description>files with BEAGLE or SHAPEIT</description>

  <requirements>
      <requirement type="package" >pandas</requirement>
      <requirement type="package" >pysam</requirement>
      <requirement type="package" >beagle</requirement>
      <requirement type="package" >shapeit</requirement>
  </requirements>

  <command><![CDATA[
    #if $input.is_of_type('vcf_bgzip')
      ln -fs $input input.vcf.gz &&
      ln -fs $input.metadata.tabix_index input.vcf.gz.tbi &&
    #end if
    #if $input.is_of_type('vcf')
      ln -fs $input input.vcf &&
    #end if
    python $__tool_directory__/vcf_phase.py
            --phase-algorithm $phase.phase_algorithm
            --out $output
            --out-format $out_format

            #if $input.is_of_type('vcf_bgzip')
               --vcf input.vcf.gz
            #end if

            #if $input.is_of_type('vcf')
               --vcf input.vcf
            #end if

            #if $model_file
              --model-file $model_file
              --model $model
            #end if

            #if $phase.phase_algorithm == 'beagle'
              --beagle-path $__tool_data_path__/shared/jars/
              #if $phase.beagle_iter
                --beagle-iter $phase.beagle_iter
              #end if
              #if $phase.beagle_burn_iter
                --beagle-burn-iter $phase.beagle_burn_iter
              #end if
              #if $phase.beagle_states
                --beagle-states $phase.beagle_states
              #end if
              #if $phase.beagle_window
                --beagle-window $phase.beagle_window
              #end if
              #if $phase.beagle_overlap
                --beagle-overlap $phase.beagle_overlap
              #end if
              #if $phase.beagle_error
                --beagle-error $phase.beagle_error
              #end if
              #if $phase.beagle_step
                --beagle-step $phase.beagle_step
              #end if
              #if $phase.beagle_nsteps
                --beagle-nsteps $phase.beagle_nsteps
              #end if
            #end if

            #if $phase.phase_algorithm == 'shapeit'
              #if $phase.shapeit_burn_iter
                --shapeit-burn-iter $phase.shapeit_burn_iter
              #end if
              #if $phase.shapeit_prune_iter
                --shapeit-prune-iter $phase.shapeit_prune_iter
              #end if
              #if $phase.shapeit_main_iter
                --shapeit-main-iter $phase.shapeit_main_iter
              #end if
              #if $phase.shapeit_states
                --shapeit-states $phase.shapeit_states
              #end if
              #if $phase.shapeit_window
                --shapeit-window $phase.shapeit_window
              #end if
            #end if

            #if $common.genetic_map
              --genetic-map $common.genetic_map
            #end if

            #if $common.ne
              --Ne $common.ne
            #end if

            #if $common.random_seed
              --random-seed $common.random_seed
            #end if

            #if $common.phase_chr
              --phase-chr $common.phase_chr
            #end if

            #if $common.phase_from_bp
              --phase-from-bp $common.phase_from_bp
            #end if

            #if $common.phase_to_bp
              --phase-to-bp $common.phase_to_bp
            #end if


  ]]></command>

  <inputs>

    <param format="vcf,vcf_bgzip" name="input" type="data" label="VCF Input"/>

    <param format="model" name="model_file" type="data" label="Model Input" optional="True"/>
    <param name="model" type="select" label="Select Model" refresh_on_change="True" optional="True">
      <options>
        <filter type="data_meta" ref="model_file" key="models"/>
      </options>
    </param>

    <conditional name="phase">
      <param name="phase_algorithm" type="select" label="Phase Algorithm" refresh_on_change='True'>
        <option value="beagle" selected="True" >Beagle</option>
        <option value="shapeit">SHAPEIT</option>
      </param>
      <when value="beagle">
        <param name="beagle_burn_iter" type="integer" label="Burn-in iterations" optional="True"/>
        <param name="beagle_iter" type="integer" label="Post burn-in iterations" optional="True"/>
        <param name="beagle_states" type="integer" label="Model states for genotype estimation" optional="True"/>
        <param name="beagle_window" type="float" label="Sliding window size (cM)" optional="True"/>
        <param name="beagle_overlap" type="float" label="Overlap between neighboring sliding windows (cM)" optional="True"/>
        <param name="beagle_error" type="float" label="HMM allele mismatch probability" optional="True"/>
        <param name="beagle_step" type="float" label="Step length (cM)" optional="True" help="Used for identifying short IBS segments"/>
        <param name="beagle_nsteps" type="integer" label="Number of consecutive steps" optional="True" help="Used for identifying long IBS segments"/>
      </when>
      <when value="shapeit">
        <param name="shapeit_burn_iter" type="integer" label="Burn-in iterations" optional="True"/>
        <param name="shapeit_prune_iter" type="integer" label="Pruning iterations" optional="True"/>
        <param name="shapeit_main_iter" type="integer" label="Main iterations" optional="True"/>
        <param name="shapeit_states" type="integer" label="Conditioning states for haplotype estimation" optional="True"/>
        <param name="shapeit_window" type="float" label="Model window size (Mb)" optional="True"/>
      </when>
    </conditional>

    <section name="common" title="Common Parameters" expanded="True">
      <param name="random_seed" type="integer" label="Seed value" optional="True"/>
      <param format="text" name="genetic_map" type="data" label="Genetic Map" optional="True"/>
      <param name="ne" type="integer" label="Effective population size" optional="True"/>
      <param name="phase_chr" type="text" label="Chromosome to phase" optional="True"/>
      <param name="phase_from_bp" type="integer" label="Lower bound of sites to include" help="Only usable with a single chromosome" optional="True"/>
      <param name="phase_to_bp" type="integer" label="Upper bound of sites to include" help="Only usable with a single chromosome" optional="True"/>
    </section>

    <param name="out_format" type="select" label="Output Format">
      <option value="vcf">VCF File</option>
      <option value="vcf.gz" selected="True">bgzipped-VCF File</option>
      <option value="bcf">BCF File</option>
    </param>

  </inputs>
  <outputs>

    <data name="output" format="vcf_bgzip">
      <change_format>
        <when input="out_format" value="vcf" format="vcf"/>
        <when input="out_format" value="bcf" format="bcf"/>
      </change_format>
    </data>

  </outputs>

  <help>
      VCF Phaser Help Text
  </help>

</tool>