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1 <tool id="shapeit_phase" name="shapeit_phase" version="0.1.0">
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2 <description>genomic data with or without reference panel</description>
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3
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4 <requirements>
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5 <requirement type="package" version="v2.r790">shapeit</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10
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11 <command><![CDATA[
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12 shapeit
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13
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14 #if $input_files.input_type_select == "vcf":
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15 --input-vcf ${input_files.vcf_file}
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16 #else if $input_files.input_type_select == "plink_ped_map":
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17 --input-ped ${input_files.plink_ped} ${input_files.plink_map}
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18 #if $input_files.plink_missing_code != "0":
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19 --missing_code $input_files.plink_missing_code
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20 #end if
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21 #else if $input_files.input_type_select == "plink_bed_bim_fam":
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22 --input-bed ${input_files.plink_bed} ${input_files.plink_bim} ${input_files.plink_fam}
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23 #else if $input_files.inputy_type_select == "oxford_gen_sample":
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24 --input-gen ${input_files.oxford_gen} ${input_files.oxford_sample}
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25 #if $input_files.oxford_threshold != "0.9":
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26 --input-thr $input_files.oxford_threshold
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27 #end if
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28 #end if
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29
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30 #if $use_genetic_map.use_genetic_map_select == "use_genetic_map_yes":
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31 --input-map $use_genetic_map.genetic_map
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32 #else if $use_genetic_map.rho != "0.0004":
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33 --rho $use_genetic_map.rho
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34 #end if
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35
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36 #if $use_ref_panel.use_ref_panel_select == "use_ref_panel_yes":
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37 --input-ref $use_ref_panel.ref_panel_haps $use_ref_panel.ref_panel_legend $use_ref_panel.ref_panel_sample
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38 #if $use_ref_panel.disable_mcmc_iterations == "disable_mcmc_iterations_yes":
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39 --no-mcmc
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40 #end if
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41 #if $use_ref_panel.filter_groups == "exclude_groups":
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42 --exclude-grp $use_ref_panel.filter_groups.exclude_groups_file
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43 #else if $use_ref_panel.filter_groups == "include_groups":
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44 --include-grp $use_ref_panel.filter_groups.include_groups_file
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45 #end if
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46 #end if
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47
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48 #if $use_filters.use_filters_select == "use_filters_yes":
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49 #if $use_filters.use_input_from == "use_input_from_yes":
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50 --input-from $input_from
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51 #end if
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52 #if $use_filters.use_input_to == "use_input_to_yes":
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53 --input-to $input_to
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54 #end if
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55 #if $use_filters.use_output_from == "use_output_from_yes":
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56 --output-from $output_from
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57 #end if
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58 #if $use_filters.use_output_to == "use_output_to_yes":
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59 --output-to $output_to
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60 #end if
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61 #if $use_filters.filter_individuals == "exclude_individuals":
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62 --exclude-ind $use_filters.exclude_inviduals_file
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63 #else if $use_filters.filter_individuals == "include_individuals":
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64 --include-ind $use_filters.include_inviduals_file
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65 #end if
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66 #if $use_filters.filter_individuals == "exclude_SNPs":
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67 --exclude-snp $use_filters.exclude_SNPs_file
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68 #else if $use_filters.filter_SNPs == "include_SNPs":
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69 --include-snp $use_filters.include_SNPs_file
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70 #end if
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71 #end if
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72
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73 #if $use_advanced_parameters.use_advanced_parameters_select == "use_advanced_parameters_yes":
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74 #if $use_advanced_parameters.chrX == "chrX_yes":
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75 --chrX
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76 #end if
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77 #if $use_advanced_parameters.noped == "noped_yes":
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78 --noped
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79 #end if
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80 #if $use_advanced_parameters.states != "100":
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81 --states $use_advanced_parameters.states
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82 #end if
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83 #if $use_advanced_parameters.window != "2.0":
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84 --window $use_advanced_parameters.window
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85 #end if
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86 #if $use_advanced_parameters.model_version1 == "use_v1_yes":
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87 --model-version1
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88 #end if
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89 #if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_european":
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90 --effective-size 11418
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91 #else if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_african":
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92 --effective-size 17469
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93 #else if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_asian":
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94 --effective-size 14269
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95 #else if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_mixedpop":
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96 --effective-size $use_advanced_parameters.eff_size.eff_size_mixed
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97 #end if
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98 #if $use_advanced_parameters.burn != "7":
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99 --burn $use_advanced_parameters.burn
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100 #end if
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101 #if $use_advanced_parameters.prune != "8":
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102 --prune $use_advanced_parameters.prune
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103 #end if
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104 #if $use_advanced_parameters.main != "20":
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105 --main $use_advanced_parameters.main
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106 #end if
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107 #if $use_advanced_parameters.threads != "1":
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108 --threads $use_advanced_parameters.threads
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109 #end if
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110 #if $use_advanced_parameters.set_rng_seed.set_rng_seed_select == "set_rng_seed_yes":
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111 --seed $use_advanced_parameters.rng_seed
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112 #end if
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113 #end if
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114 --output-max $out_haps $out_sample
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115 --output-graph $out_graph
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116 --output-log $out_log
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117 ]]></command>
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118
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119 <inputs>
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120 <conditional name="input_files">
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121 <param name="input_type_select" type="select" label="Please specify your input files.">
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122 <option value="vcf" selected="True">VCF Variant Call Format</option>
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123 <option value="plink_ped_map">Plink PED/MAP format</option>
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124 <option value="plink_bed_bim_fam">Plink BED/BIM/FAM format</option>
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125 <option value="oxford_gen_sample">Oxford GEN/SAMPLE format</option>
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126 </param>
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127 <when value="plink_ped_map">
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128 <param name="plink_ped" type="data" label="Specify text genotype file (.ped)"/>
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129 <param name="plink_map" type="data" label="Specify SNP map file (.map)"/>
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130 <param name="plink_missing_code" type="text" label="Missing data labeled as" value="0" default="0"/>
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131 </when>
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132 <when value="plink_bed_bim_fam">
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133 <param name="plink_bed" type="data" label="Specify binary genotype file (.bed)"/>
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134 <param name="plink_bim" type="data" label="Specify SNP map file (.bim)"/>
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135 <param name="plink_fam" type="data" label="Specify individual information file (.fam)"/>
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136 </when>
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137 <when value="oxford_gen_sample">
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138 <param name="oxford_gen" type="data" label="Specify text genotype file (.gen)"/>
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139 <param name="oxford_sample" type="data" label="Specify individual information file (.sample)"/>
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140 <param name="oxford_threshold" type="float" label="SNP Probability threshold" default="0.9" value="0.9"/>
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141 </when>
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142 <when value="vcf">
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143 <param name="vcf_file" type="data" label="Specify Variant Call Format file (.vcf)"/>
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144 </when>
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145 </conditional>
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146
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147 <conditional name="use_genetic_map">
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148 <param name="use_genetic_map_select" type="select" label="Do you want to use a genetic map?">
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149 <option value="use_genetic_map_yes" selected="True">Yes</option>
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150 <option value="use_genetic_map_no">No</option>
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151 </param>
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152 <when value="use_genetic_map_yes">
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153 <param name="genetic_map" type="data" label="Genetic map file (.gmap)" />
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154 </when>
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155 <when value="use_genetic_map_no">
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156 <param name="rho" type="float" value="0.0004" default="0.0004" label="Adjust recombination rate (--rho) for human data (0.001)"/>
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157 </when>
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158 </conditional>
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159
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160 <conditional name="use_ref_panel">
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161 <param name="use_ref_panel_select" type="select" label="Do you want to use a reference panel?">
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162 <option value="use_ref_panel_yes">Use a reference panel</option>
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163 <option value="use_ref_panel_no" selected="True">Do not use reference panel</option>
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164 </param>
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165 <when value="use_ref_panel_yes">
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166 <param name="ref_panel_haps" type="data" label="Specify reference haplotypes file (.haps)" />
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167 <param name="ref_panel_legend" type="data" label="Specify SNP map file (.legend)" />
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168 <param name="ref_panel_sample" type="data" label="Specify individual information file (.sample)" />
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169
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170 <conditional name="disable_mcmc_iterations">
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171 <param name="disable_mcmc_iterations_select" type="select" label="Disable MCMC iterations">
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172 <option value="disable_mcmc_iterations_yes">Yes</option>
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173 <option value="disable_mcmc_iterations_no" selected="True">No</option>
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174 </param>
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175 </conditional>
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176
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177 <conditional name="filter_groups">
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178 <param name="filter_groups_select" type="select" label="Do you want to filter groups?">
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179 <option value="no_individual_filter" selected="True">No filtering</option>
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180 <option value="exclude_groups">Exclude list of groups</option>
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181 <option value="include_groups">Limit list of groups</option>
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182 </param>
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183 <when value="exclude_groups">
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184 <param name="exclude_inviduals_file" type="data" label="Specify file with excluded groups (.exc)"/>
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185 </when>
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186 <when value="include_groups">
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187 <param name="include_inviduals_file" type="data" label="Specify file with limited groups (.inc)"/>
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188 </when>
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189 </conditional>
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190
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191 </when>
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192 </conditional>
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193
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194 <conditional name="use_advanced_parameters">
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195 <param name="use_advanced_parameters_select" type="select" label="Set parameters">
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196 <option value="use_advanced_parameters_yes">Use advanced parameters</option>
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197 <option value="use_advanced_parameters_no" selected="True">Use standard parameters</option>
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198 </param>
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199
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200 <when value="use_advanced_parameters_yes">
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201 <param name="chrX" type="select" label="Use X chromosomal genotypes?">
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202 <option value="chrX_yes">Yes</option>
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203 <option value="chrX_no" selected="True">No</option>
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204 </param>
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205
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206 <param name="noped" type="select" label="Discard pedigree/family information?">
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207 <option value="noped_yes">Yes</option>
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208 <option value="noped_no" selected="True">No</option>
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209 </param>
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210
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211 <param name="states" type="integer" label="Number of conditioning haplotypes used during phasing (--states)" default="100" value="100"/>
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212 <param name="window" type="float" label="Window size [Mb] in which conditioning haplotypes are defined" default="2.0" value="2.0"/>
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213 <param name="model_version1" type="select" label="Use SHAPEIT v1 graphical model">
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214 <option value="use_v1_yes">Yes</option>
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215 <option value="use_v1_no" selected="True">No</option>
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216 </param>
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217
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218 <conditional name="eff_size">
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219 <param name="eff_size_select" type="select" label="Effective population size for phasing">
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220 <option value="eff_size_european">European population (11418)</option>
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221 <option value="eff_size_african">African population (17469)</option>
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222 <option value="eff_size_asian">Asian population (14269)</option>
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223 <option value="eff_size_mixed_option" selected="True">Mixed population</option>
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224 </param>
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225 <when value="eff_size_mixed_option">
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226 <param name="eff_size_mixed" type="integer" label="Specify effective population size, depending on proportions [11418,17469]" default="14443" value="14443"/>
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227 </when>
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228 </conditional>
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229
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230 <param name="burn" type="integer" default="7" value="7" label="Number of burn-in iterations to find good starting point"/>
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231 <param name="prune" type="integer" default="8" value="8" label="Number of pruning iterations to find parsimonious graphs"/>
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232 <param name="main" type="integer" default="20" value="20" label="Number of iterations to compute transition probabilities"/>
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233 <param name="threads" type="integer" default="1" value="1" label="Specify number of threads"/>
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234
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235 <conditional name="set_rng_seed">
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236 <param name="set_rng_seed_select" type="select" label="Set seed for random number generator (RNG)">
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237 <option value="set_rng_seed_yes">Yes</option>
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238 <option value="set_rng_seed_no" selected="True">No</option>
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239 </param>
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240 <when value="set_rng_seed_yes">
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241 <param name="rng_seed" type="integer" default="18011981" value="18011981" label="RNG seed" />
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242 </when>
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243 </conditional>
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244 </when>
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245 </conditional>
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246
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247 <conditional name="use_filters">
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248 <param name="use_filters_select" type="select" label="Apply filtering">
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249 <option value="use_filters_yes">Yes</option>
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250 <option value="use_filters_no" selected="True">No</option>
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251 </param>
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252 <when value="use_filters_yes">
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253
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254 <conditional name="use_input_from">
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255 <param name="use_input_from_select" type="select" label="Only consider genotypes above a position?">
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256 <option value="use_input_from_yes">Yes</option>
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257 <option value="use_input_from_no" selected="True">No</option>
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258 </param>
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259 <when value="use_input_from_yes">
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260 <param name="input_from" type="integer" value="1" default="1" label="Set position:"/>
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261 </when>
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262 </conditional>
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263
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264 <conditional name="use_input_to">
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265 <param name="use_input_to_select" type="select" label="Only consider genotypes above a position?">
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266 <option value="use_input_to_yes">Yes</option>
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267 <option value="use_input_to_no" selected="True">No</option>
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268 </param>
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269 <when value="use_input_to_yes">
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270 <param name="input_to" type="integer" value="1" default="1" label="Set position:"/>
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271 </when>
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272 </conditional>
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273
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274 <conditional name="use_output_from">
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275 <param name="use_output_from_select" type="select" label="Only output genotypes above a position?">
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276 <option value="use_output_from_yes">Yes</option>
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277 <option value="use_output_from_no" selected="True">No</option>
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278 </param>
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279 <when value="use_output_from_yes">
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280 <param name="output_from" type="integer" value="1" default="1" label="Set position:"/>
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281 </when>
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282 </conditional>
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283
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284 <conditional name="use_output_to">
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285 <param name="use_output_to_select" type="select" label="Only output genotypes above a position?">
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286 <option value="use_output_to_yes">Yes</option>
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287 <option value="use_output_to_no" selected="True">No</option>
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288 </param>
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289 <when value="use_output_to_yes">
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290 <param name="output_to" type="integer" value="1" default="1" label="Set position:"/>
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291 </when>
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292 </conditional>
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293
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294 <conditional name="filter_individuals">
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295 <param name="filter_individuals_select" type="select" label="Do you want to filter individuals?">
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296 <option value="no_individual_filter" selected="True">No filtering</option>
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297 <option value="exclude_individuals">Exclude list of individuals</option>
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298 <option value="include_individuals">Limit list of individuals</option>
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299 </param>
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300 <when value="exclude_individuals">
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301 <param name="exclude_inviduals_file" type="data" label="Specify file with excluded individuals (.exc)"/>
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302 </when>
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303 <when value="include_individuals">
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304 <param name="include_inviduals_file" type="data" label="Specify file with limited individuals (.inc)"/>
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305 </when>
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306 </conditional>
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307
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308 <conditional name="filter_SNPs">
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309 <param name="filter_SNPs_select" type="select" label="Do you want to filter SNPs?">
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310 <option value="no_individual_filter" selected="True">No filtering</option>
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311 <option value="exclude_SNPs">Exclude list of SNPs</option>
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312 <option value="include_SNPs">Limit list of SNPs</option>
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313 </param>
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314 <when value="exclude_SNPs">
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315 <param name="exclude_inviduals_file" type="data" label="Specify file with excluded SNPs (.exc)"/>
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316 </when>
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317 <when value="include_SNPs">
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318 <param name="include_inviduals_file" type="data" label="Specify file with limited SNPs (.inc)"/>
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319 </when>
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320 </conditional>
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321 </when>
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322 </conditional>
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323
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324 </inputs>
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325 <outputs>
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326 <data name="out_haps" format="tabular" label="${tool.name} on ${on_string} haplotypes (.haps)"/>
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327 <data name="out_sample" format="tabular" label="${tool.name} on ${on_string} additional information (.sample)"/>
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328 <data name="out_graph" format="text" label="${tool.name} on ${on_string} haplotype graphs (.hgraph)"/>
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329 <data name="out_log" format="text" label="${tool.name} on ${on_string} logfile (.log)"/>
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330 </outputs>
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331 <help><![CDATA[
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332 TODO: Fill in help.
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333 ]]></help>
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334 </tool>
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