Mercurial > repos > iuc > bcftools_csq

annotate bcftools_csq.xml @ 20:0ab4bbd0f9b5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:49:22 +0000
parents 10da4a86ee5c
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1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Haplotype aware consequence predictor</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">csq</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements">
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9 <expand macro="samtools_requirement"/>
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10 </expand>
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11 <expand macro="version_command"/>
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12 <command detect_errors="aggressive"><![CDATA[
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13 @PREPARE_INPUT_FILE@
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14 #set $section = $sec_required.reference_source
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15 @PREPARE_FASTA_REF@
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17 #set $section = $sec_restrict
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18 @PREPARE_TARGETS_FILE@
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19 @PREPARE_REGIONS_FILE@
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21 bcftools @EXECUTABLE@
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23 ## csq required inputs section
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24 #set $section = $sec_required.reference_source
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25 @FASTA_REF@
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26 --gff-annot '$sec_required.gff_annot'
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28 ## csq options section
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29 #if str($sec_csq_opts.ncsq):
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30 --ncsq $sec_csq_opts.ncsq
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31 #end if
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32 $sec_csq_opts.local_csq
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33 #if $sec_csq_opts.phase:
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34 --phase $sec_csq_opts.phase
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35 #end if
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36 #if str($sec_csq_opts.custom_tag):
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37 --custom-tag '$sec_csq_opts.custom_tag'
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38 #end if
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39 #if str($sec_csq_opts.trim_protein_seq)
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40 --trim-protein-seq $sec_csq_opts.trim_protein_seq
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41 #end if
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42 #if $sec_csq_opts.genetic_code
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43 --genetic-code '$sec_csq_opts.genetic_code'
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44 #end if
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46 ## Subset section
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47 #set $section = $sec_subset
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48 @SAMPLES@
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49
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50 ## Filter section
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51 #set $section = $sec_restrict
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52 @INCLUDE@
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53 @EXCLUDE@
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54 @REGIONS@
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55 @TARGETS@
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56
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57 @OUTPUT_TYPE@
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58
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59 ## Primary Input/Outputs
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60 @INPUT_FILE@
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61 > '$output_file'
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62
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63 ]]>
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64 </command>
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65 <inputs>
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66 <expand macro="macro_input"/>
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67 <section name="sec_required" expanded="true" title="Required References">
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68 <expand macro="macro_fasta_ref"/>
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69 <param name="gff_annot" type="data" format="gff3" label="GFF3 annotation file" help="From Ensembl: ftp://ftp.ensembl.org/pub/current_gff3/"/>
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70 </section>
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71 <section name="sec_csq_opts" expanded="true" title="CSQ Options">
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72 <param name="ncsq" type="integer" value="16" min="1" max="50" label="maximum number of consequences to consider per site" help="-ncsq 16"/>
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73 <param name="local_csq" type="boolean" truevalue="--local-csq" falsevalue="" checked="false" label="run localized predictions considering only one VCF record at a time" help="--local-csq switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time"/>
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74 <param name="phase" type="select" optional="true" label="phase" help="how to construct haplotypes and how to deal with unphased data">
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75 <option value="a">take GTs as is, create haplotypes regardless of phase (0/1 -&gt; 0|1)</option>
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76 <option value="m">merge *all* GTs into a single haplotype (0/1 -&gt; 1, 1/2 -&gt; 1)</option>
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77 <option value="r">require phased GTs, throw an error on unphased het GTs</option>
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78 <option value="R">create non-reference haplotypes if possible (0/1 -&gt; 1|1, 1/2 -&gt; 1|2)</option>
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79 <option value="s">skip unphased GTs</option>
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80 </param>
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81 <param name="custom_tag" type="text" value="" optional="true" label="use this custom tag to store consequences rather than the default BCSQ tag">
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82 <validator type="regex" message="">^(\w+)?$</validator>
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83 </param>
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84 <param argument="--trim-protein-seq" type="integer" min="0" value="" optional="true" label="Abbreviate protein-changing predictions" help="Abbreviate protein-changing predictions to max INT aminoacids"/>
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85 <param argument="--genetic-code" type="select" optional="true" label="Genetic code table" help="Choose a predefined genetic code table used to translate coding sequences. Leave unset for the default bcftools behaviour.">
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86 <option value="0">0: Standard simplified</option>
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87 <option value="1">1: Standard</option>
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88 <option value="2">2: Vertebrate mitochondrial</option>
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89 <option value="3">3: Yeast mitochondrial</option>
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90 <option value="4">4: Mold, Protozoan, Coelenterate mitochondrial; Mycoplasma; Spiroplasma</option>
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91 <option value="5">5: Invertebrate mitochondrial</option>
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92 <option value="6">6: Ciliate, Dasycladacean and Hexamita nuclear</option>
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93 <option value="9">9: Echinoderm and Flatworm mitochondrial</option>
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94 <option value="10">10: Euplotid nuclear</option>
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95 <option value="11">11: Bacterial, Archaeal and Plant plastid</option>
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96 <option value="12">12: Alternative yeast nuclear</option>
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97 <option value="13">13: Ascidian mitochondrial</option>
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98 <option value="14">14: Alternative flatworm mitochondrial</option>
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99 <option value="15">15: Blepharisma nuclear</option>
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100 <option value="16">16: Chlorophycean mitochondrial</option>
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101 <option value="21">21: Trematode mitochondrial</option>
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102 <option value="22">22: Scenedesmus obliquus mitochondrial</option>
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103 <option value="23">23: Thraustochytrium mitochondrial</option>
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104 <option value="24">24: Pterobranchia mitochondrial</option>
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105 <option value="25">25: Candidate Division SR1 and Gracilibacteria</option>
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106 <option value="26">26: Pachysolen tannophilus nuclear</option>
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107 <option value="27">27: Karyorelict nuclear</option>
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108 <option value="28">28: Condylostoma nuclear</option>
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109 <option value="29">29: Mesodinium nuclear</option>
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110 <option value="30">30: Peritrich nuclear</option>
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111 <option value="31">31: Blastocrithidia nuclear</option>
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112 <option value="33">33: Cephalodiscidae mitochondrial UAA-Tyr</option>
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113 </param>
0
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114 </section>
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115 <section name="sec_restrict" expanded="false" title="Restrict to">
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116 <expand macro="macro_region_restrict"/>
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117 <expand macro="macro_target_restrict"/>
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118 <expand macro="macro_include"/>
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119 <expand macro="macro_exclude"/>
0
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120 </section>
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121 <section name="sec_subset" expanded="false" title="Subset Options">
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122 <expand macro="macro_samples"/>
0
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123 </section>
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124 <expand macro="macro_select_output_type"/>
0
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125 </inputs>
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126 <outputs>
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127 <expand macro="macro_vcf_output"/>
0
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128 </outputs>
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129 <tests>
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130 <test>
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131 <param name="input_file" ftype="vcf" value="csq.vcf"/>
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132 <section name="sec_required">
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133 <expand macro="test_using_reference" ref="csq.fa"/>
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134 </section>
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135 <section name="sec_required">
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136 <param name="gff_annot" ftype="gff3" value="csq.gff3"/>
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137 </section>
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138 <param name="output_type" value="v"/>
0
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139 <output name="output_file">
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140 <assert_contents>
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141 <has_text text="BCSQ"/>
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142 </assert_contents>
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143 </output>
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144 </test>
4
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145 <test>
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146 <param name="input_file" ftype="vcf" value="csq.vcf"/>
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147 <section name="sec_required">
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148 <expand macro="test_using_reference" select_from="cached" ref="csq"/>
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149 </section>
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150 <section name="sec_required">
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151 <param name="gff_annot" ftype="gff3" value="csq.gff3"/>
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152 </section>
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153 <param name="output_type" value="v"/>
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154 <output name="output_file">
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155 <assert_contents>
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156 <has_text text="BCSQ"/>
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157 </assert_contents>
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158 </output>
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159 </test>
13
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160 <!-- Test protein seq prediction-->
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161 <test>
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162 <param name="input_file" ftype="vcf" value="csq.vcf"/>
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163 <section name="sec_required">
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164 <expand macro="test_using_reference" select_from="cached" ref="csq"/>
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165 </section>
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166 <section name="sec_required">
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167 <param name="gff_annot" ftype="gff3" value="csq.gff3"/>
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168 </section>
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169 <param name="output_type" value="v"/>
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170 <section name="sec_csq_opts">
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171 <param name="trim_protein_seq" value="10"/>
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172 <param name="genetic_code" value="1"/>
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173 </section>
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174 <output name="output_file">
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175 <assert_contents>
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176 <has_text text="BCSQ"/>
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177 </assert_contents>
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178 </output>
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179 <assert_command>
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180 <has_text text="--trim-protein-seq"/>
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181 <has_text text="--genetic-code '1'"/>
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182 </assert_command>
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183 </test>
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184 <!-- Test region overlap-->
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185 <test>
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186 <param name="input_file" ftype="vcf" value="csq.vcf"/>
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187 <section name="sec_required">
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188 <expand macro="test_using_reference" select_from="cached" ref="csq"/>
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189 </section>
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190 <section name="sec_required">
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191 <param name="gff_annot" ftype="gff3" value="csq.gff3"/>
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192 </section>
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193 <param name="output_type" value="v"/>
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194 <section name="sec_restrict">
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195 <conditional name="regions">
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196 <param name="regions_src" value="regions" />
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197 <repeat name="region_specs">
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198 <param name="chrom" value="1" />
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199 </repeat>
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200 </conditional>
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201 </section>
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202 <output name="output_file">
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203 <assert_contents>
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204 <has_text text="BCSQ"/>
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205 </assert_contents>
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206 </output>
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207 <assert_command>
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208 <has_text text="--regions-overlap"/>
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209 </assert_command>
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210 </test>
0
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211 </tests>
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212 <help><![CDATA[
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213 =====================================
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214 bcftools @EXECUTABLE@
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215 =====================================
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216
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217 Haplotype aware consequence predictor which correctly handles combined variants such as MNPs split over
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218 multiple VCF records, SNPs separated by an intron (but adjacent in the spliced transcript) or nearby
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219 frame-shifting indels which in combination in fact are not frame-shifting.
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220
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221 The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the -c option).
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222 The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes. See the usage examples
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223 below for using the %TBCSQ converter in query for extracting a more human readable form from this bitmask.
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224 The contruction of the bitmask limits the number of consequences that can be referenced in the FORMAT/BCSQ tags.
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225 By default this is 16, but if more are required, see the --ncsq option.
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226
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227 The program requires on input a VCF/BCF file, the reference genome in fasta format (--fasta-ref)
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228 and genomic features in the GFF3 format downloadable from the Ensembl website (--gff-annot),
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229 and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3 files are supported.
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230
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231 By default, the input VCF should be phased. If phase is unknown, or only partially known,
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232 the --phase option can be used to indicate how to handle unphased data. Alternatively,
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233 haplotype aware calling can be turned off with the --local-csq option.
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234
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235 If conflicting (overlapping) variants within one haplotype are detected, a warning will
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236 be emitted and predictions will be based on only the first variant in the analysis.
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237
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238 Symbolic alleles are not supported. They will remain unannotated in the output VCF and are
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239 ignored for the prediction analysis.
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240
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241
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242 @REGIONS_HELP@
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243 @TARGETS_HELP@
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244
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245 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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246
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247 @BCFTOOLS_HOWTOS@
0
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248 ]]>
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249 </help>
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250 <expand macro="citations"/>
0
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251 </tool>