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1 <tool id="bcftools_view" name="bcftools view" version="0.0.1">
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2 <description>Converts BCF format to VCF format</description>
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3 <requirements>
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4 <requirements type="package">samtools</requirements>
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5 </requirements>
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6 <command interpreter="python">
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7 bcftools_view.py bcftools view
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8 #if str( $A ) == "true":
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9 -A
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10 #end if
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11 #if str( $b ) == "true":
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12 -b
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13 #end if
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14 #if $D.seq_dictionary == "true":
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15 -D "$D.input"
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16 #end if
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17 #if str( $F ) == "true":
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18 -F
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19 #end if
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20 #if str( $G ) == "true":
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21 -G
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22 #end if
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23 #if str( $N ) == "true":
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24 -N
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25 #end if
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26 #if str( $S ) == "true":
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27 -S
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28 #end if
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29 #if str( $u) == "true":
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30 -u
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31 #end if
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32 #if str( $c ) == "true":
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33 -c
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34 #end if
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35 #if str( $e ) == "true":
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36 -e
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37 #end if
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38 #if str( $g ) == "true":
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39 -g
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40 #end if
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41 #if $i.alt_indel_snp_ratio == "true":
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42 -i $i.ratio
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43 #end if
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44 #if $p.variant_filter == "true":
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45 -p $p.float_value
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46 #end if
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47 #if $t.mutation_rate == "true":
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48 -t $t.rate
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49 #end if
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50 #if str( $v ) == "true":
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51 -v
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52 #end if
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53 $input
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54 > $output
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55 </command>
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56 <inputs>
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57 <param name="input" type="data" format="bcf" label="Choose a bcf file to view" />
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58 <param name="A" type="select" label="Retain all possible alternate alleles at variant sites">
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59 <option value="true">Yes</option>
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60 <option value="false" selected="true">No</option>
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61 </param>
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62 <param name="b" type="select" label="Output in the BCF format. The default is VCF.">
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63 <option value="true">Yes</option>
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64 <option value="false" selected="true">No</option>
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65 </param>
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66 <conditional name="D">
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67 <param name="seq_dictionary" type="select" label="Sequence dictionary (list of chromosome names) for VCF->BCF conversion.">
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68 <option value="true">Yes</option>
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69 <option value="false" selected="true">No</option>
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70 </param>
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71 <when value="true">
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72 <param name="input" type="data" format="tabular" label="Sequence dictionary" />
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73 </when>
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74 </conditional>
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75 <param name="F" type="select" label="Indicate PL is generated by r921 or before (ordering is different).">
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76 <option value="true">Yes</option>
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77 <option value="false" selected="true">No</option>
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78 </param>
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79 <param name="G" type="select" label="Suppress all individual genotype information.">
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80 <option value="true">Yes</option>
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81 <option value="false" selected="true">No</option>
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82 </param>
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83 <param name="N" type="select" label="Skip sites where the REF field is not A/C/G/T">
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84 <option value="true">Yes</option>
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85 <option value="false" selected="true">No</option>
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86 </param>
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87 <param name="S" type="select" label="The input is VCF instead of BCF.">
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88 <option value="true">Yes</option>
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89 <option value="false" selected="true">No</option>
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90 </param>
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91 <param name="u" type="select" label="Uncompressed BCF output.">
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92 <option value="true">Yes</option>
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93 <option value="false" selected="true">No</option>
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94 </param>
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95 <param name="c" type="select" label="Call variants using Bayesian inference. Automatically performs max-likelihood inference only">
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96 <option value="true" selected="true">Yes</option>
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97 <option value="false">No</option>
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98 </param>
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99 <param name="e" type="select" label="Perform max-likelihood inference only, including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT.">
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100 <option value="true">Yes</option>
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101 <option value="false" selected="true">No</option>
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102 </param>
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103 <param name="g" type="select" label="Call per-sample genotypes at variant sites">
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104 <option value="true" selected="true">Yes</option>
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105 <option value="false">No</option>
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106 </param>
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107 <conditional name="i">
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108 <param name="alt_indel_snp_ratio" type="select" label="Use alternate INDEL-to-SNP mutation rate, default 0.15.">
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109 <option value="true">Yes</option>
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110 <option value="false" selected="true">No</option>
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111 </param>
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112 <when value="true">
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113 <param name="ratio" type="float" label="Ratio (float)" value="0.15" />
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114 </when>
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115 </conditional>
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116 <conditional name="p">
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117 <param name="variant_filter" type="select" >
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118 <option value="true">Yes</option>
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119 <option value="false" selected="true">No</option>
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120 </param>
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121 <when value="true">
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122 <param name="float_value" type="float" label="Float" value="0.5" />
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123 </when>
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124 </conditional>
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125 <conditional name="t">
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126 <param name="mutation_rate" type="select" label="Specify scaled mutation rate for variant calling, default is 0.001.">
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127 <option value="true">Yes</option>
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128 <option value="false" selected="true">No</option>
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129 </param>
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130 <when value="true">
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131 <param name="rate" type="float" label="Mutation Rate (float)" value="0.001" />
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132 </when>
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133 </conditional>
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134 <param name="v" type="select" label="Output variant sites only.">
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135 <option value="true" selected="true">Yes</option>
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136 <option value="false">No</option>
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137 </param>
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138 </inputs>
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139 <outputs>
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140 <data format="tabular" name="output" />
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141 </outputs>
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142 <help>
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143 **What it does:**
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144
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145 This tool converts BCF files into VCF files using BCFtools view from the SAMtools set of utilities:
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146
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147 http://samtools.sourceforge.net/samtools.shtml#4
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148
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149
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150 </help>
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151 </tool>
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