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1 <tool id="bcftools_filter" name="BCFtools filter" version="1.0.0">
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2 <description>Apply fixed-threshold filters</description>
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23
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3 <requirements>
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4 <requirement type="package" version="1.3">bcftools</requirement>
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5 </requirements>
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11
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6 <command>
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7 #if str( $input_file_index ) != "None":
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8 ln -s -f $input input_file.${input.ext} &&
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9 ln -s -f $input_file_index input_file.${input.ext}.tbi &&
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10 #end if
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11
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12 bcftools filter
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13 --output "${output_file}"
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14 --output-type "${output_type}"
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15 #if str( $regions_file ) != "None":
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16 --regions-file "${regions_file}"
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17 #end if
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18 #if str( $regions ) != "":
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19 --regions "${regions}"
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20 #end if
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21 #if str( $targets_file ) != "None":
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22 --targets-file "${targets_file}"
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23 #end if
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24 #if str( $targets ) != "":
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25 --targets "${targets}"
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26 #end if
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27 #if str( $expr_cond.set_expr ) == "True":
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28 #if str( $expr_cond.include_or_exclude ) == "include":
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29 --include "${expr_cond.expr}"
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30 #else
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31 --exclude "${expr_cond.expr}"
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32 #end if
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33 #end if
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34 #if str( $mode_plus ) == "true":
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35 #if str( $mode_x ) == "true":
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36 --mode +x
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37 #else
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38 --mode +
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39 #end if
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40 #elif str( $mode_x ) == "true"
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41 --mode x
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42 #end if
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43 #if str( $soft_filter_cond.set_soft_filter ) == "True":
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44 #if str( $soft_filter_cond.string_or_plus_cond.string_or_plus ) == "use_plus":
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45 --soft-filter +
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46 #else
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47 --soft-filter "${soft_filter_cond.string_or_plus_cond.str}"
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48 #end if
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49 #end if
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50 #if str( $set_gts_cond.set_gts ) == "True":
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51 #if str( $set_gts_cond.gts ) == "period":
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52 --set-GTs .
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53 #else
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54 --set-GTs 0
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55 #end if
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56 #end if
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57
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58 #if str( $input_file_index ) != "None":
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59 input_file.${input.ext}
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60 #else
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61 $input
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62 #end if
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63 </command>
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64 <inputs>
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65 <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/>
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66 <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/>
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67 <param name="output_type" type="select" label="Output data type">
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68 <option value="v" selected="true">VCF</option>
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69 <option value="b">BCF</option>
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70 </param>
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71 <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
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72 <param name="regions" type="text" size="80" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
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73 <sanitizer invalid_char="">
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74 <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
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75 </sanitizer>
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76 </param>
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77 <param name="targets_file" type="data" optional="true" label="Targets file" help="-T. Targets specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
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78 <param name="targets" type="text" size="80" optional="True" label="Targets list" help="-t. Comma-separated list of targets. Format: [^]chr|chr:pos|chr:from-to|chr:from-[,...]">
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79 <sanitizer invalid_char="">
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80 <valid initial="string.digits"><add value="CHRchr-:,^"/> </valid>
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81 </sanitizer>
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82 </param>
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83 <conditional name="expr_cond">
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84 <param name="set_expr" type="boolean" checked="False" label="Filter by expression" help="-i, e. Include/ exclude sites for which expression is true. Must use valid expression."/>
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85 <when value="true">
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86 <param name="include_or_exclude" type="select" label="Include or exclude by expression">
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87 <option value="include">Include</option>
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88 <option value="exclude">Exclude</option>
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89 </param>
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90 <param name="expr" type="text" size="80" label="Expression">
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91 <sanitizer invalid_char="">
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92 <valid initial="string.letters,string.digits"><add value="~`!@#$%^&*()-_=+[{]}\|;:'",<.>?/ " /> </valid>
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93 </sanitizer>
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94 </param>
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95 </when>
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96 </conditional>
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97 <param name="mode_x" type="boolean" checked="False" label="For sites that pass filter, reset filter to "PASS"" help="-m x. Default: When FILTER string is empty, set filter to "PASS". Do not change FILTER string otherwise."/>
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98 <param name="mode_plus" type="boolean" checked="False" label="For sites that fail filter, append new FILTER string to existing FILTER string" help="-m +. Default: Replace existing FILTER string with new FILTER string."/>
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99 <conditional name="soft_filter_cond">
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100 <param name="set_soft_filter" type="boolean" checked="False" label="Annotate FILTER column" help="-s"/>
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101 <when value="true">
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102 <conditional name="string_or_plus_cond">
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103 <param name="string_or_plus" type="select" label="Annotation string">
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104 <option value="use_plus" selected="true">Annotate with a pre-generated unique string ("Filter1", "Filter2", etc.)</option>
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105 <option value="use_str">Choose annotation string</option>
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106 </param>
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107 <when value="use_str">
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108 <param name="str" type="text" size="80" label="String to annotate with" />
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109 </when>
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110 </conditional>
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111 </when>
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112 </conditional>
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113 <conditional name="set_gts_cond">
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114 <param name="set_gts" type="boolean" checked="False" label="Set genotype of samples that fail filter" help="-S"/>
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115 <when value="true">
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116 <param name="gts" type="select" label="Genotype of failed samples">
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117 <option value="period" selected="true">.</option>
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118 <option value="ref_allele">Reference allele</option>
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119 </param>
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120 </when>
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121 </conditional>
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122 </inputs>
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123 <outputs>
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124 <data name="output_file" format="vcf" label="${tool.name} on ${on_string}">
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125 <change_format>
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126 <when input="output_type" value="b" format="bcf" />
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127 </change_format>
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128 </data>
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129 </outputs>
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130 <help>
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131 **About this tool**
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132
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133 **BCFtools filter**: Apply fixed-threshold filters.
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134
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135 Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
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136 </help>
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137 </tool>
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