Mercurial > repos > sanbi-uwc > shapeit_phase
changeset 0:97363f287de1 draft
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
| author | sanbi-uwc |
|---|---|
| date | Fri, 14 Sep 2018 01:08:00 -0400 |
| parents | |
| children | 497594b1d2f4 |
| files | shapeit_phase.xml |
| diffstat | 1 files changed, 411 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/shapeit_phase.xml Fri Sep 14 01:08:00 2018 -0400 @@ -0,0 +1,411 @@ +<tool id="shapeit_phase" name="shapeit_phase" version="0.2.0"> + <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" format="txt" label="Specify text genotype file (.ped)"/> + <param name="plink_map" type="data" format="txt" label="Specify SNP map file (.map)"/> + <param name="plink_missing_code" type="text" label="Missing data labeled as" value="0"/> + </when> + <when value="plink_bed_bim_fam"> + <param name="plink_bed" type="data" format="binary" label="Specify binary genotype file (.bed)"/> + <param name="plink_bim" type="data" format="txt" label="Specify SNP map file (.bim)"/> + <param name="plink_fam" type="data" format="txt" 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" format="txt" label="Specify text genotype file (.gen)"/> + <param name="oxford_sample" type="data" format="txt" label="Specify individual information file (.sample)"/> + <param name="oxford_threshold" type="float" label="SNP Probability threshold" value="0.9"/> + </when> + <when value="vcf"> + <param name="vcf_file" type="data" format="vcf" 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" format="txt" label="Genetic map file (.gmap)" /> + </when> + </conditional> + </when> + <when value="use_genetic_map_no"> + <param name="rho" type="float" value="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" format="data" label="Specify reference haplotypes file (.haps)" /> + <param name="ref_panel_legend" type="data" format="data" label="Specify SNP map file (.legend)" /> + <param name="ref_panel_sample" type="data" format="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> + <when value="disable_mcmc_iterations_yes"></when> + <when value="disable_mcmc_iterations_no"></when> + </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="no_individual_filter"></when> + <when value="exclude_groups"> + <param name="exclude_inviduals_file" type="data" format="txt" label="Specify file with excluded groups (.exc)"/> + </when> + <when value="include_groups"> + <param name="include_inviduals_file" type="data" format="txt" label="Specify file with limited groups (.inc)"/> + </when> + </conditional> + + </when> + <when value="use_ref_panel_no"> + </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)" value="100"/> + <param name="window" type="float" label="Window size [Mb] in which conditioning haplotypes are defined" 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_european"></when> + <when value="eff_size_african"></when> + <when value="eff_size_asian"></when> + <when value="eff_size_mixed_option"> + <param name="eff_size_mixed" type="integer" label="Specify effective population size, depending on proportions [11418,17469]" value="14443"/> + </when> + </conditional> + + <param name="burn" type="integer" value="7" label="Number of burn-in iterations to find good starting point"/> + <param name="prune" type="integer" value="8" label="Number of pruning iterations to find parsimonious graphs"/> + <param name="main" type="integer" value="20" label="Number of iterations to compute transition probabilities"/> + <param name="threads" type="integer" 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" value="18011981" label="RNG seed" /> + </when> + <when value="set_rng_seed_no"></when> + </conditional> + </when> + <when value="use_advanced_parameters_no"></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" label="Set position:"/> + </when> + <when value="use_input_from_no"></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" label="Set position:"/> + </when> + <when value="use_input_to_no"></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" label="Set position:"/> + </when> + <when value="use_output_from_no"></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" label="Set position:"/> + </when> + <when value="use_output_to_no"></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="no_individual_filter"></when> + <when value="exclude_individuals"> + <param name="exclude_inviduals_file" type="data" format="txt" label="Specify file with excluded individuals (.exc)"/> + </when> + <when value="include_individuals"> + <param name="include_inviduals_file" type="data" format="txt" 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="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> + + </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> + <citations> + <citation type="doi">10.1038/nmeth.1785</citation> + </citations> +</tool>