# HG changeset patch # User sanbi-uwc # Date 1536901680 14400 # Node ID 97363f287de1c095c0edf567ad6e305c7bdeb7f1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56 diff -r 000000000000 -r 97363f287de1 shapeit_phase.xml --- /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 @@ + + genomic data with or without reference panel + + + shapeit + + + + + + &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 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1038/nmeth.1785 + +