Mercurial > repos > iuc > bcftools_csq

annotate bcftools_csq.xml @ 11:6014ca4c359f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
author iuc
date Sat, 15 Jan 2022 13:17:45 +0000
parents 3d1eee0f806a
children aed58f2684fe
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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="@TOOL_VERSION@">
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3 <description>Haplotype aware consequence predictor</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">csq</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="bio_tools" />
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9 <expand macro="requirements">
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10 <expand macro="samtools_requirement"/>
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11 </expand>
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12 <expand macro="version_command" />
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13 <command detect_errors="aggressive"><![CDATA[
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14 @PREPARE_ENV@
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15 @PREPARE_INPUT_FILE@
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16 #set $section = $sec_required.reference_source
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17 @PREPARE_FASTA_REF@
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19 #set $section = $sec_restrict
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20 @PREPARE_TARGETS_FILE@
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21 @PREPARE_REGIONS_FILE@
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23 bcftools @EXECUTABLE@
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25 ## csq required inputs section
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26 #set $section = $sec_required.reference_source
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27 @FASTA_REF@
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28 --gff-annot '$sec_required.gff_annot'
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30 ## csq options section
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31 #if str($sec_csq_opts.ncsq):
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32 --ncsq $sec_csq_opts.ncsq
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33 #end if
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34 $sec_csq_opts.local_csq
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35 #if $sec_csq_opts.phase:
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36 --phase $sec_csq_opts.phase
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37 #end if
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38 #if str($sec_csq_opts.custom_tag):
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39 --custom-tag '$sec_csq_opts.custom_tag'
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40 #end if
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42 ## Subset section
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43 #set $section = $sec_subset
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44 @SAMPLES@
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45
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46 ## Filter section
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47 #set $section = $sec_restrict
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48 @INCLUDE@
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49 @EXCLUDE@
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50 @REGIONS@
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51 @TARGETS@
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52
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53 @OUTPUT_TYPE@
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54
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55 ## Primary Input/Outputs
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56 @INPUT_FILE@
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57 > '$output_file'
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58
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59 ]]>
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60 </command>
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61 <inputs>
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62 <expand macro="macro_input" />
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63 <section name="sec_required" expanded="true" title="Required References">
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64 <expand macro="macro_fasta_ref" />
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65 <param name="gff_annot" type="data" format="gff3" label="GFF3 annotation file"
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66 help="From Ensembl: ftp://ftp.ensembl.org/pub/current_gff3/"/>
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67 </section>
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68 <section name="sec_csq_opts" expanded="true" title="CSQ Options">
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69 <param name="ncsq" type="integer" value="16" min="1" max="50" label="maximum number of consequences to consider per site"
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70 help="-ncsq 16"/>
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71 <param name="local_csq" type="boolean" truevalue="--local-csq" falsevalue="" checked="false" label="run localized predictions considering only one VCF record at a time"
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72 help="--local-csq switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time"/>
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73 <param name="phase" type="select" optional="true" label="phase"
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74 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 -> 0|1)</option>
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76 <option value="m">merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 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 -> 1|1, 1/2 -> 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"
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82 label="use this custom tag to store consequences rather than the default BCSQ tag">
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83 <validator type="regex" message="">^(\w+)?$</validator>
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84 </param>
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85 </section>
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86
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87 <section name="sec_restrict" expanded="false" title="Restrict to">
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88 <expand macro="macro_restrict" />
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89 <expand macro="macro_restrict" type="target" label_type="Target" />
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90 <expand macro="macro_include" />
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91 <expand macro="macro_exclude" />
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92 </section>
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93 <section name="sec_subset" expanded="false" title="Subset Options">
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94 <expand macro="macro_samples" />
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95 </section>
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96 <expand macro="macro_select_output_type" />
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97 </inputs>
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98 <outputs>
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99 <expand macro="macro_vcf_output" />
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100 </outputs>
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101 <tests>
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102 <test>
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103 <param name="input_file" ftype="vcf" value="csq.vcf" />
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104 <expand macro="test_using_reference" ref="csq.fa" />
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105 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
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106 <param name="output_type" value="v" />
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107 <output name="output_file">
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108 <assert_contents>
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109 <has_text text="BCSQ" />
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110 </assert_contents>
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111 </output>
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112 </test>
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113 <test>
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114 <param name="input_file" ftype="vcf" dbkey="?" value="csq.vcf" />
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115 <expand macro="test_using_reference" select_from="cached" ref="csq" />
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116 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
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117 <param name="output_type" value="v" />
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118 <output name="output_file">
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119 <assert_contents>
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120 <has_text text="BCSQ" />
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121 </assert_contents>
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122 </output>
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123 </test>
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124
0
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125 </tests>
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126 <help><![CDATA[
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127 =====================================
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128 bcftools @EXECUTABLE@
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129 =====================================
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130
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131 Haplotype aware consequence predictor which correctly handles combined variants such as MNPs split over
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132 multiple VCF records, SNPs separated by an intron (but adjacent in the spliced transcript) or nearby
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133 frame-shifting indels which in combination in fact are not frame-shifting.
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134
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135 The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the -c option).
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136 The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes. See the usage examples
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137 below for using the %TBCSQ converter in query for extracting a more human readable form from this bitmask.
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138 The contruction of the bitmask limits the number of consequences that can be referenced in the FORMAT/BCSQ tags.
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139 By default this is 16, but if more are required, see the --ncsq option.
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140
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141 The program requires on input a VCF/BCF file, the reference genome in fasta format (--fasta-ref)
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142 and genomic features in the GFF3 format downloadable from the Ensembl website (--gff-annot),
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143 and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3 files are supported.
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144
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145 By default, the input VCF should be phased. If phase is unknown, or only partially known,
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146 the --phase option can be used to indicate how to handle unphased data. Alternatively,
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147 haplotype aware calling can be turned off with the --local-csq option.
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148
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149 If conflicting (overlapping) variants within one haplotype are detected, a warning will
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150 be emitted and predictions will be based on only the first variant in the analysis.
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151
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152 Symbolic alleles are not supported. They will remain unannotated in the output VCF and are
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153 ignored for the prediction analysis.
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154
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155
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156 @REGIONS_HELP@
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157 @TARGETS_HELP@
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158
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159 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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160
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161 @BCFTOOLS_WIKI@
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162 ]]>
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163 </help>
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164 <expand macro="citations" />
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165 </tool>