gistfile1.txt

<tool id="shapeit_phase" name="shapeit_phase" version="0.1.0">
    <description>genomic data with or without reference panel</description>

    <requirements>
        <requirement type="package" version="v2.r790">shapeit</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command><![CDATA[
        #if str($use_ref_panel) == "use_ref_panel_yes" and str($use_ref_panel.ref_panel_from_table) == "ref_panel_from_table_yes" and str($input_files.input_type_select) == 'plink_bed_bim_fam_list':
          # this is all expecting 1000GP-style reference data
          PART=`head -1 myfile.bim | cut -f1` && 
          REF_DIR='${use_genetic_map.map_from_table.fields.path}' &&
          REF_PREFIX='${use_genetic_map.map_from_table.fields.reference_prefix}' &&
          if [ -f "\${REF_DIR}/\${REF_PREFIX}_\${PART}.hap.gz" ] \; then
            HAP="\${REF_DIR}/\${REF_PREFIX}_\${PART}.hap.gz" &&
            LEGEND="\${REF_DIR}/\${REF_PREFIX}_\${PART}.legend.gz" &&
            SAMPLE="\${REF_DIR}/\${REF_PREFIX}.sample" ;
          fi &&
          MAP_PREFIX='${use_genetic_map.map_from_table.fields.map_prefix}' &&
          MAP=`ls \${REF_DIR}/\${MAP_PREFIX}_\${PART}_*` &&
          if [ ! -f "\${MAP}" ] ; then
            echo "Failed to find valid map file at \${MAP}" >&2 &&
            exit 1 ; 
          fi &&
        # end 

        shapeit

        #if $input_files.input_type_select == "vcf":
          --input-vcf ${input_files.vcf_file}
        #else if $input_files.input_type_select == "plink_ped_map":
          --input-ped ${input_files.plink_ped} ${input_files.plink_map}
          #if $input_files.plink_missing_code != "0":
            --missing_code $input_files.plink_missing_code
          #end if
        #else if $input_files.input_type_select == "plink_bed_bim_fam":
          --input-bed ${input_files.plink_bed} ${input_files.plink_bim} ${input_files.plink_fam}
        #else if $input_files.input_type_select == "plink_bed_bim_fam_list":
          --input-bed '${input_files.plink_bed_etc_list}[0]' '${input_files.plink_bed_etc_list}[1]' '${input_files.plink_bed_etc_list}[2]'
        #else if $input_files.inputy_type_select == "oxford_gen_sample":
          --input-gen ${input_files.oxford_gen} ${input_files.oxford_sample}
          #if $input_files.oxford_threshold != "0.9":
            --input-thr $input_files.oxford_threshold
          #end if
        #end if

        #if $use_genetic_map.use_genetic_map_select == "use_genetic_map_yes":
          #if $use_genetic_map.genetic_map_from_table == "genetic_map_from_table_yes":
            --input-map \$MAP
          else:
            --input-map $use_genetic_map.genetic_map
          #end if
        #else if $use_genetic_map.rho != "0.0004":
          --rho $use_genetic_map.rho
        #end if

        #if $use_ref_panel.use_ref_panel_select == "use_ref_panel_yes":
          #if $use_ref_panel.ref_panel_from_table == "ref_panel_from_table_yes":
            --input-ref \$HAP \$LEGEND \$SAMPLE
          #else
            --input-ref $use_ref_panel.ref_panel_haps $use_ref_panel.ref_panel_legend $use_ref_panel.ref_panel_sample
          #end if
          #if $use_ref_panel.disable_mcmc_iterations == "disable_mcmc_iterations_yes":
            --no-mcmc
          #end if
          #if $use_ref_panel.filter_groups == "exclude_groups":
            --exclude-grp $use_ref_panel.filter_groups.exclude_groups_file
          #else if $use_ref_panel.filter_groups == "include_groups":
              --include-grp $use_ref_panel.filter_groups.include_groups_file
          #end if
        #end if

        #if $use_filters.use_filters_select == "use_filters_yes":
          #if $use_filters.use_input_from == "use_input_from_yes":
            --input-from $input_from
          #end if
          #if $use_filters.use_input_to == "use_input_to_yes":
            --input-to $input_to
          #end if
          #if $use_filters.use_output_from == "use_output_from_yes":
            --output-from $output_from
          #end if
          #if $use_filters.use_output_to == "use_output_to_yes":
            --output-to $output_to
          #end if
          #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
          #end if
          #if $use_advanced_parameters.states != "100":
            --states $use_advanced_parameters.states
          #end if
          #if $use_advanced_parameters.window != "2.0":
            --window $use_advanced_parameters.window
          #end if
          #if $use_advanced_parameters.model_version1 == "use_v1_yes":
            --model-version1
          #end if
          #if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_european":
            --effective-size 11418
          #else if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_african":
            --effective-size 17469
          #else if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_asian":
            --effective-size 14269
          #else if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_mixedpop":
            --effective-size $use_advanced_parameters.eff_size.eff_size_mixed
          #end if
          #if $use_advanced_parameters.burn != "7":
            --burn $use_advanced_parameters.burn
          #end if
          #if $use_advanced_parameters.prune != "8":
            --prune $use_advanced_parameters.prune
          #end if
          #if $use_advanced_parameters.main != "20":
            --main $use_advanced_parameters.main
          #end if
          #if $use_advanced_parameters.threads != "1":
            --threads $use_advanced_parameters.threads
          #end if
          #if $use_advanced_parameters.set_rng_seed.set_rng_seed_select == "set_rng_seed_yes":
            --seed $use_advanced_parameters.rng_seed
          #end if
        #end if
        --output-max $out_haps $out_sample
        --output-graph $out_graph
        --output-log $out_log
    ]]></command>

    <inputs>
      <conditional name="input_files">
        <param name="input_type_select" type="select" label="Please specify your input files.">
          <option value="vcf" selected="True">VCF Variant Call Format</option>
          <option value="plink_ped_map">Plink PED/MAP format</option>
          <option value="plink_bed_bim_fam">Plink BED/BIM/FAM format</option>
          <option value="plink_bed_bim_fam_list">Plink BED/BIM/FAM format list</option>
          <option value="oxford_gen_sample">Oxford GEN/SAMPLE format</option>
        </param>
        <when value="plink_ped_map">
          <param name="plink_ped" type="data" label="Specify text genotype file (.ped)"/>
          <param name="plink_map" type="data" label="Specify SNP map file (.map)"/>
          <param name="plink_missing_code" type="text" label="Missing data labeled as" value="0" default="0"/>
        </when>
        <when value="plink_bed_bim_fam">
          <param name="plink_bed" type="data" label="Specify binary genotype file (.bed)"/>
          <param name="plink_bim" type="data" label="Specify SNP map file (.bim)"/>
          <param name="plink_fam" type="data" label="Specify individual information file (.fam)"/>
        </when>
        <when value="plink_bed_bim_fam_list">
          <param name="plink_bed_etc_list" type="data_collection" collection_type="list" label="BED/BIM/FAM files as a collection (list)" />
        </when>
        <when value="oxford_gen_sample">
          <param name="oxford_gen" type="data" label="Specify text genotype file (.gen)"/>
          <param name="oxford_sample" type="data" label="Specify individual information file (.sample)"/>
          <param name="oxford_threshold" type="float" label="SNP Probability threshold" default="0.9" value="0.9"/>
        </when>
        <when value="vcf">
          <param name="vcf_file" type="data" label="Specify Variant Call Format file (.vcf)"/>
        </when>
      </conditional>

      <conditional name="use_genetic_map">
        <param name="use_genetic_map_select" type="select" label="Do you want to use a genetic map?">
          <option value="use_genetic_map_yes" selected="True">Yes</option>
          <option value="use_genetic_map_no">No</option>
        </param>
        <when value="use_genetic_map_yes">
          <conditional name="genetic_map_from_table">
            <param name="genetic_map_from_table_select" type="select" label="Use built in data?">
              <option value="genetic_map_from_table_yes" selected="True">Yes</option>
              <option value="genetic_map_from_table_no">No</option>
            </param>
            <when value="genetic_map_from_table_yes">
              <param name="map_from_table" type="select" label="Select reference map">
                <options from_data_table="shapeit_ref" />
              </param>
            </when>
            <when value="genetic_map_from_table_no">
              <param name="genetic_map" type="data" label="Genetic map file (.gmap)" />
            </when>
          </conditional>
        </when>
        <when value="use_genetic_map_no">
          <param name="rho" type="float" value="0.0004" default="0.0004" label="Adjust recombination rate (--rho) for human data (0.001)"/>
        </when>
      </conditional>

      <conditional name="use_ref_panel">
        <param name="use_ref_panel_select" type="select" label="Do you want to use a reference panel?">
          <option value="use_ref_panel_yes">Use a reference panel</option>
          <option value="use_ref_panel_no" selected="True">Do not use reference panel</option>
        </param>
        <when value="use_ref_panel_yes">
          <conditional name="ref_panel_from_table">
            <param name="ref_panel_from_table_select" type="select" label="Use built in data?">
              <option value="ref_panel_from_table_yes" selected="True">Yes</option>
              <option value="ref_panel_from_table_no">No</option>
            </param>
            <when value="ref_panel_from_table_yes">
              <param name="ref_from_table" type="select" label="Select reference panel">
                <options from_data_table="shapeit_ref" />
              </param>
            </when>
            <when value="ref_panel_from_table_no">            
              <param name="ref_panel_haps" type="data" label="Specify reference haplotypes file (.haps)" />
              <param name="ref_panel_legend" type="data" label="Specify SNP map file (.legend)" />
              <param name="ref_panel_sample" type="data" label="Specify individual information file (.sample)" />
            </when>
          </conditional>
          <conditional name="disable_mcmc_iterations">
            <param name="disable_mcmc_iterations_select" type="select" label="Disable MCMC iterations">
              <option value="disable_mcmc_iterations_yes">Yes</option>
              <option value="disable_mcmc_iterations_no" selected="True">No</option>
            </param>
          </conditional>

          <conditional name="filter_groups">
            <param name="filter_groups_select" type="select" label="Do you want to filter groups?">
              <option value="no_individual_filter" selected="True">No filtering</option>
              <option value="exclude_groups">Exclude list of groups</option>
              <option value="include_groups">Limit list of groups</option>
            </param>
            <when value="exclude_groups">
              <param name="exclude_inviduals_file" type="data" label="Specify file with excluded groups (.exc)"/>
            </when>
            <when value="include_groups">
              <param name="include_inviduals_file" type="data" label="Specify file with limited groups (.inc)"/>
            </when>
          </conditional>

        </when>
      </conditional>

      <conditional name="use_advanced_parameters">
        <param name="use_advanced_parameters_select" type="select" label="Set parameters">
          <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>

          <param name="noped" type="select" label="Discard pedigree/family information?">
            <option value="noped_yes">Yes</option>
            <option value="noped_no" selected="True">No</option>
          </param>

          <param name="states" type="integer" label="Number of conditioning haplotypes used during phasing (--states)" default="100" value="100"/>
          <param name="window" type="float" label="Window size [Mb] in which conditioning haplotypes are defined" default="2.0" value="2.0"/>
          <param name="model_version1" type="select" label="Use SHAPEIT v1 graphical model">
            <option value="use_v1_yes">Yes</option>
            <option value="use_v1_no" selected="True">No</option>
          </param>

          <conditional name="eff_size">
            <param name="eff_size_select" type="select" label="Effective population size for phasing">
              <option value="eff_size_european">European population (11418)</option>
              <option value="eff_size_african">African population (17469)</option>
              <option value="eff_size_asian">Asian population (14269)</option>
              <option value="eff_size_mixed_option" selected="True">Mixed population</option>
            </param>
            <when value="eff_size_mixed_option">
              <param name="eff_size_mixed" type="integer" label="Specify effective population size, depending on proportions [11418,17469]" default="14443" value="14443"/>
            </when>
          </conditional>

          <param name="burn" type="integer" default="7" value="7" label="Number of burn-in iterations to find good starting point"/>
          <param name="prune" type="integer" default="8" value="8" label="Number of pruning iterations to find parsimonious graphs"/>
          <param name="main" type="integer" default="20" value="20" label="Number of iterations to compute transition probabilities"/>
          <param name="threads" type="integer" default="1" value="1" label="Specify number of threads"/>

          <conditional name="set_rng_seed">
            <param name="set_rng_seed_select" type="select" label="Set seed for random number generator (RNG)">
              <option value="set_rng_seed_yes">Yes</option>
              <option value="set_rng_seed_no" selected="True">No</option>
            </param>
            <when value="set_rng_seed_yes">
              <param name="rng_seed" type="integer" default="18011981" value="18011981" label="RNG seed" />
            </when>
          </conditional>
        </when>
      </conditional>

      <conditional name="use_filters">
        <param name="use_filters_select" type="select" label="Apply filtering">
          <option value="use_filters_yes">Yes</option>
          <option value="use_filters_no" selected="True">No</option>
        </param>
        <when value="use_filters_yes">

          <conditional name="use_input_from">
            <param name="use_input_from_select" type="select" label="Only consider genotypes above a position?">
              <option value="use_input_from_yes">Yes</option>
              <option value="use_input_from_no" selected="True">No</option>
            </param>
            <when value="use_input_from_yes">
              <param name="input_from" type="integer" value="1" default="1" label="Set position:"/>
            </when>
          </conditional>

          <conditional name="use_input_to">
            <param name="use_input_to_select" type="select" label="Only consider genotypes above a position?">
              <option value="use_input_to_yes">Yes</option>
              <option value="use_input_to_no" selected="True">No</option>
            </param>
            <when value="use_input_to_yes">
              <param name="input_to" type="integer" value="1" default="1" label="Set position:"/>
            </when>
          </conditional>

          <conditional name="use_output_from">
            <param name="use_output_from_select" type="select" label="Only output genotypes above a position?">
              <option value="use_output_from_yes">Yes</option>
              <option value="use_output_from_no" selected="True">No</option>
            </param>
            <when value="use_output_from_yes">
              <param name="output_from" type="integer" value="1" default="1" label="Set position:"/>
            </when>
          </conditional>

          <conditional name="use_output_to">
            <param name="use_output_to_select" type="select" label="Only output genotypes above a position?">
              <option value="use_output_to_yes">Yes</option>
              <option value="use_output_to_no" selected="True">No</option>
            </param>
            <when value="use_output_to_yes">
              <param name="output_to" type="integer" value="1" default="1" label="Set position:"/>
            </when>
          </conditional>

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

    </inputs>
    <outputs>
      <data name="out_haps" format="tabular" label="${tool.name} on ${on_string} haplotypes (.haps)"/>
      <data name="out_sample" format="tabular" label="${tool.name} on ${on_string} additional information (.sample)"/>
      <data name="out_graph" format="text" label="${tool.name} on ${on_string} haplotype graphs (.hgraph)"/>
      <data name="out_log" format="text" label="${tool.name} on ${on_string} logfile (.log)"/>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>