Mercurial > repos > jjohnson > bcftools_call

annotate bcftools_call.xml @ 0:20b3aaa16d64 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:46:24 -0400
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20b3aaa16d64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
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3 <description>SNP/indel variant calling from VCF/BCF</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">call</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="aggressive"><![CDATA[
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11 @PREPARE_ENV@
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12 @PREPARE_INPUT_FILE@
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13 #set $section = $sec_consensus_variant_calling.variant_calling
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14 #set $targets_path = None
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15 #if $section.method == 'multiallelic':
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16 #if $section.genotypes.constrain == 'alleles':
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17 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
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18 @PREPARE_TARGETS_FILE@
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19 #end if
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20 #end if
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21
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22 bcftools @EXECUTABLE@
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23
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24 #set $section = $sec_consensus_variant_calling.variant_calling
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25 #if $section.method == 'multiallelic':
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26 -m
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27 #if str($section.gvcf) != '':
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28 --gvcf $section.gvcf
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29 #end if
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30 #if $section.genotypes.constrain == 'alleles':
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31 --constrain alleles $section.genotypes.insert_missed
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32 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
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33 @TARGETS_FILE@
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34 #else
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35 #if $section.genotypes.constrain == 'trio':
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36 --constrain trio
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37 #if $section.genotypes.novel_rate:
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38 --novel-rate '$section.genotypes.novel_rate'
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39 #end if
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40 #end if
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41 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
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42 @TARGETS@
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43 #end if
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44 #else
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45 -c
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46 #end if
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47
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48 #set $section = $sec_restrict
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49 @REGIONS@
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50 @SAMPLES@
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51
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52 #set $section = $sec_consensus_variant_calling
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53 #if $section.pval_threshold:
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54 --pval-threshold "$section.pval_threshold"
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55 #end if
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56 #if $section.prior:
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57 --prior "$section.prior"
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58 #end if
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59
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60 ## File format section
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61 #set $section = $sec_file_format
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62 #if $section.ploidy:
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63 --ploidy "${section.ploidy}"
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64 #end if
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65 #if $section.ploidy_file:
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66 --ploidy-file "${section.ploidy_file}"
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67 #end if
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68
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69 ## Input/output section
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70 #set $section = $sec_input_output
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71 ${section.keep_alts}
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72 ## #if section.format_fields:
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73 ## --format-fields "${section.format_fields}"
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74 ## #end if
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75 ${section.keep_masked_ref}
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76 #if $section.skip_variants:
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77 --skip-variants "${section.skip_variants}"
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78 #end if
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79 ${section.variants_only}
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80
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81 @OUTPUT_TYPE@
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82 @THREADS@
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83
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84 ## Primary Input/Outputs
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85 @INPUT_FILE@
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86 > "$output_file"
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87 ]]>
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88 </command>
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89 <inputs>
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90 <expand macro="macro_input" />
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91 <section name="sec_restrict" expanded="false" title="Restrict to">
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92 <expand macro="macro_regions" />
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93 <expand macro="macro_samples" />
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94 </section>
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95 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
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96 <conditional name="variant_calling">
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97 <param name="method" type="select" label="calling method">
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98 <option value="multiallelic">Multiallelic and rare-variant Caller</option>
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99 <option value="consensus">Consensus Caller</option>
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100 </param>
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101 <when value="multiallelic">
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102 <conditional name="genotypes">
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103 <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)">
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104 <option value="none">Do not constrain</option>
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105 <option value="alleles">alleles - call genotypes given alleles</option>
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106 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
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107 </param>
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108 <when value="none">
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109 <expand macro="macro_targets" />
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110 </when>
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111 <when value="alleles">
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112 <expand macro="macro_targets_file"/>
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113 <param name="insert_missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert Missed" help="output also sites missed by mpileup but present in -T" />
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114 </when>
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115 <when value="trio">
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116 <expand macro="macro_targets" />
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117 <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
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118 </when>
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119 </conditional>
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120 <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
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121 </when>
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122 <when value="consensus">
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123 <conditional name="genotypes">
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124 <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)">
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125 <option value="none">Do not constrain</option>
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126 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
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127 </param>
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128 <when value="none">
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129 </when>
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130 <when value="trio">
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131 <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
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132 </when>
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133 </conditional>
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134 <expand macro="macro_targets" />
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135 </when>
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136 </conditional>
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137 <param name="pval_threshold" type="float" label="Pval Threshold" default="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" />
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138 <param name="prior" type="float" label="Prior" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" />
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139 </section>
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140 <section name="sec_file_format" expanded="false" title="File format Options">
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141 <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true">
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142 <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option>
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143 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option>
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144 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option>
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145 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
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146 <option value="1">1 - Treat all samples as haploid</option>
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147 </param>
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148 <param name="ploidy_file" type="data" format="tabular" label="Ploidy File" optional="True" help="space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
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149 <expand macro="macro_regions" />
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150 <expand macro="macro_samples" />
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151 </section>
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152 <section name="sec_input_output" expanded="false" title="Input/output Options">
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153 <param name="keep_alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep Alts" help="keep all possible alternate alleles at variant sites" />
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154 <param name="format_fields" type="text" value="" optional="true" label="Format Fields"
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155 help="output format fields: GQ,GP" >
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156 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator>
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157 </param>
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158 <param name="keep_masked_ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep Masked Ref" help="keep sites with masked reference allele (REF=N)" />
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159 <param name="skip_variants" type="select" label="Skip Variants" optional="True" help="skip indels/snps">
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160 <option value="indels">indels</option>
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161 <option value="snps">snps</option>
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162 </param>
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163 <param name="variants_only" type="boolean" truevalue="--variants-only" falsevalue="" label="Variants Only" help="output variant sites only" />
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164 </section>
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165 <expand macro="macro_select_output_type" />
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166 </inputs>
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167 <outputs>
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168 <expand macro="macro_vcf_output"/>
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169 </outputs>
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170 <tests>
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171 <test>
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172 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
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173 <param name="method" value="multiallelic" />
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174 <param name="variants_only" value="true" />
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175 <param name="output_type" value="v" />
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176 <output name="output_file">
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177 <assert_contents>
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178 <has_text text="DP4=2,4,8,11;MQ=49" />
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179 </assert_contents>
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180 </output>
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181 </test>
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182 <test>
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183 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
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184 <param name="method" value="multiallelic" />
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185 <param name="gvcf" value="0" />
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186 <param name="output_type" value="v" />
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187 <output name="output_file">
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188 <assert_contents>
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189 <has_text text="MinDP" />
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190 <has_text text="DP4=2,4,8,11;MQ=49" />
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191 </assert_contents>
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192 </output>
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193 </test>
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194 <test>
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195 <param name="input_file" ftype="vcf" value="mpileup.X.vcf" />
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196 <param name="method" value="multiallelic" />
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197 <param name="ploidy_file" value="mpileup.ploidy" />
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198 <param name="samples_file" value="mpileup.samples" />
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199 <param name="output_type" value="v" />
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200 <output name="output_file">
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201 <assert_contents>
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202 <has_text text="DP4=2,4,8,11;MQ=49" />
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203 </assert_contents>
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204 </output>
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205 </test>
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206 <test>
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207 <param name="input_file" ftype="vcf" value="mpileup.X.vcf" />
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208 <param name="method" value="consensus" />
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209 <param name="output_type" value="v" />
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210 <param name="ploidy_file" value="mpileup.ploidy" />
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211 <output name="output_file">
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212 <assert_contents>
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213 <has_text text="DP4=2,4,8,11" />
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214 <has_text text="PV4=1,1,1,1" />
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215 </assert_contents>
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216 </output>
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217 </test>
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218 </tests>
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219 <help><![CDATA[
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220 ==================================
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221 bcftools @EXECUTABLE@
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222 ==================================
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223
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224 SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup.
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225
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226 - This command replaces the former "bcftools view" caller.
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227 - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand.
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228 - The original calling model can be invoked with the -c option.
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229
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230 @REGIONS_HELP@
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231 @TARGETS_HELP@
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232
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233 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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234
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235 @BCFTOOLS_WIKI@
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236 ]]>
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237 </help>
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238 <expand macro="citations" />
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239 </tool>