Mercurial > repos > iuc > bcftools_csq

annotate bcftools_csq.xml @ 3:40388f544e5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 13:09:13 -0400
parents 039ea3f1dea9
children f10f5b4e7854
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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@+galaxy1">
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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="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_ENV@
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14 @PREPARE_INPUT_FILE@
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15 #set $section = $sec_required.reference_source
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16 @PREPARE_FASTA_REF@
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18 #set $section = $sec_restrict
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19 @PREPARE_TARGETS_FILE@
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20 @PREPARE_REGIONS_FILE@
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22 bcftools @EXECUTABLE@
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24 ## csq required inputs section
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25 #set $section = $sec_required.reference_source
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26 @FASTA_REF@
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27 --gff-annot '$sec_required.gff_annot'
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29 ## csq options section
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30 #if str($sec_csq_opts.ncsq):
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31 --ncsq $sec_csq_opts.ncsq
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32 #end if
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33 $sec_csq_opts.local_csq
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34 #if $sec_csq_opts.phase:
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35 --phase $sec_csq_opts.phase
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36 #end if
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37 #if str($sec_csq_opts.custom_tag):
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38 --custom-tag '$sec_csq_opts.custom_tag'
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39 #end if
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41 ## Subset section
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42 #set $section = $sec_subset
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43 @SAMPLES@
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44
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45 ## Filter section
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46 #set $section = $sec_restrict
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47 @INCLUDE@
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48 @EXCLUDE@
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49 @REGIONS@
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50 @TARGETS@
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51
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52 @OUTPUT_TYPE@
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53
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54 ## Primary Input/Outputs
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55 @INPUT_FILE@
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56 > '$output_file'
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57
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58 ]]>
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59 </command>
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60 <inputs>
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61 <expand macro="macro_input" />
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62 <section name="sec_required" expanded="true" title="Required References">
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63 <expand macro="macro_fasta_ref" />
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64 <param name="gff_annot" type="data" format="gff3" label="GFF3 annotation file"
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65 help="From Ensembl: ftp://ftp.ensembl.org/pub/current_gff3/"/>
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66 </section>
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67 <section name="sec_csq_opts" expanded="true" title="CSQ Options">
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68 <param name="ncsq" type="integer" value="16" min="1" max="50" label="maximum number of consequences to consider per site"
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69 help="-ncsq 16"/>
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70 <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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71 help="--local-csq switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time"/>
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72 <param name="phase" type="select" optional="true" label="phase"
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73 help="how to construct haplotypes and how to deal with unphased data">
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74 <option value="a">take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)</option>
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75 <option value="m">merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)</option>
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76 <option value="r">require phased GTs, throw an error on unphased het GTs</option>
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77 <option value="R">create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)</option>
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78 <option value="s">skip unphased GTs</option>
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79 </param>
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80 <param name="custom_tag" type="text" value="" optional="true"
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81 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 </section>
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85
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86 <section name="sec_restrict" expanded="false" title="Restrict to">
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87 <expand macro="macro_restrict" />
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88 <expand macro="macro_restrict" type="target" label_type="Target" />
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89 <expand macro="macro_include" />
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90 <expand macro="macro_exclude" />
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91 </section>
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92 <section name="sec_subset" expanded="false" title="Subset Options">
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93 <expand macro="macro_samples" />
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94 </section>
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95 <expand macro="macro_select_output_type" />
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96 </inputs>
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97 <outputs>
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98 <expand macro="macro_vcf_output" />
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99 </outputs>
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100 <tests>
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101 <test>
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102 <param name="input_file" ftype="vcf" value="csq.vcf" />
3
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103 <expand macro="test_using_reference" ref="csq.fa" />
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104 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
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105 <param name="output_type" value="v" />
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106 <output name="output_file">
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107 <assert_contents>
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108 <has_text text="BCSQ" />
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109 </assert_contents>
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110 </output>
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111 </test>
3
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112 <test>
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113 <param name="input_file" ftype="vcf" dbkey="?" value="csq.vcf" />
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114 <expand macro="test_using_reference" select_from="cached" ref="csq" />
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115 <param name="gff_annot" ftype="gff3" value="csq.gff3" />
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116 <param name="output_type" value="v" />
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117 <output name="output_file">
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118 <assert_contents>
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119 <has_text text="BCSQ" />
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120 </assert_contents>
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121 </output>
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122 </test>
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123
0
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124 </tests>
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125 <help><![CDATA[
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126 =====================================
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127 bcftools @EXECUTABLE@
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128 =====================================
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129
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130 Haplotype aware consequence predictor which correctly handles combined variants such as MNPs split over
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131 multiple VCF records, SNPs separated by an intron (but adjacent in the spliced transcript) or nearby
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132 frame-shifting indels which in combination in fact are not frame-shifting.
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133
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134 The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the -c option).
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135 The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes. See the usage examples
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136 below for using the %TBCSQ converter in query for extracting a more human readable form from this bitmask.
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137 The contruction of the bitmask limits the number of consequences that can be referenced in the FORMAT/BCSQ tags.
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138 By default this is 16, but if more are required, see the --ncsq option.
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139
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140 The program requires on input a VCF/BCF file, the reference genome in fasta format (--fasta-ref)
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141 and genomic features in the GFF3 format downloadable from the Ensembl website (--gff-annot),
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142 and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3 files are supported.
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143
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144 By default, the input VCF should be phased. If phase is unknown, or only partially known,
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145 the --phase option can be used to indicate how to handle unphased data. Alternatively,
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146 haplotype aware calling can be turned off with the --local-csq option.
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147
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148 If conflicting (overlapping) variants within one haplotype are detected, a warning will
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149 be emitted and predictions will be based on only the first variant in the analysis.
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150
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151 Symbolic alleles are not supported. They will remain unannotated in the output VCF and are
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152 ignored for the prediction analysis.
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153
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154
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155 @REGIONS_HELP@
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156 @TARGETS_HELP@
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157
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158 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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159
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160 @BCFTOOLS_WIKI@
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161 ]]>
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162 </help>
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163 <expand macro="citations" />
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164 </tool>