Mercurial > repos > iuc > tb_variant_filter

annotate tb_variant_filter.xml @ 5:ee4a90760848 draft

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planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit e064fb07acad057d3df849a6f153ed6ef90837f1
author iuc
date Sun, 18 Dec 2022 17:39:30 +0000
parents e7aff4a85df5
children 32f14a2723ec
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ee4a90760848 planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit e064fb07acad057d3df849a6f153ed6ef90837f1
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1 <tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" profile="20.09">
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2 <description>M. tuberculosis H37Rv VCF filter</description>
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3 <macros>
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ee4a90760848 planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit e064fb07acad057d3df849a6f153ed6ef90837f1
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4 <token name="@TOOL_VERSION@">0.3.6</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">tb_variant_filter</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 tb_variant_filter
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11 #if "region_filter" in str($filters).split(',')
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12 #if str($filter_options.show_filter_options) == "yes":
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13 --region_filter $filter_options.region_filter
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14 #else
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15 --region_filter farhat_rlc
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16 #end if
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17 #end if
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18 #if "close_to_indel_filter" in str($filters).split(',')
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19 --close_to_indel_filter
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20 #if str($filter_options.show_filter_options) == "yes":
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21 --indel_window_size $filter_options.indel_window_size
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22 #end if
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23 #end if
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24 #if "min_percentage_alt_filter" in str($filters).split(',')
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25 --min_percentage_alt_filter
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26 #if str($filter_options.show_filter_options) == "yes":
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27 --min_percentage_alt $filter_options.min_percentage_alt
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28 #end if
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29 #end if
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30 #if "min_depth_filter" in str($filters).split(',')
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31 --min_depth_filter
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32 #if str($filter_options.show_filter_options) == "yes":
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33 --min_depth $filter_options.min_depth
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34 #end if
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35 #end if
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36 #if "snv_only_filter" in str($filters).split(','):
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37 --snv_only_filter
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38 #end if
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39 '$input1' '$output1'
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40 ]]></command>
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41 <inputs>
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42 <param type="data" name="input1" label="VCF file to be filter" format="vcf"/>
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43
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44 <param type="select" name="filters" multiple="true" label="Filters to apply">
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45 <option value="region_filter" selected="true">Filter out variants by regions</option>
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46 <option value="close_to_indel_filter">Filter variants close to indels</option>
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47 <option value="min_percentage_alt_filter">Filter variants by percentage alt allele</option>
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48 <option value="min_depth_filter">Filter sites by read alignment depth</option>
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49 <option value="snv_only_filter">Only accept SNVs</option>
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50 </param>
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51
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52 <conditional name="filter_options">
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53 <param type="select" name="show_filter_options" label="Show options for the filters">
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54 <option value="yes">Yes</option>
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55 <option value="no" selected="true">No</option>
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56 </param>
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57 <when value="yes">
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58 <param argument="--region_filter" type="select" multiple="true" label="Region filters to enable">
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59 <!-- if these are changed the code above needs to change to keep the defaults in line with those that are default here -->
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60 <option value="farhat_rlc" selected="true">Refined Low Confidence regions from Farhat lab</option>
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61 <option value="farhat_rlc_lowmap">Refined Low Confidence and Low Mappability regions from Farhat lab (for &lt; 100bp or single ended reads)</option>
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62 <option value="pe_ppe">PE/PPE</option>
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63 <option value="tbprofiler">TBProfiler antibiotic resistant genes</option>
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64 <option value="mtbseq">MTBseq antibiotic resistant genes</option>
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65 <option value="uvp">UVP repeat / insertion sequence sites</option>
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66 </param>
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67 <param argument="--indel_window_size" type="integer" value="5" label="Window to mask around indels"/>
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68 <param argument="--min_percentage_alt" type="float" value="90"
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69 label="Minimum alternate allele percentage to accept"/>
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70 <param argument="--min_depth" type="integer" value="30" label="Minimum read depth (coverage)"/>
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71 </when>
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72 <when value="no"></when>
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73
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74 </conditional>
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75 </inputs>
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76 <outputs>
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77 <data name="output1" format="vcf"/>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="input1" value="test_input1.vcf" ftype="vcf" />
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82 <param name="filters" value="region_filter" />
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83 <conditional name="filter_options">
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84 <param name="show_filter_options" value="yes" />
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85 <param name="region_filter" value="pe_ppe,tbprofiler,uvp" />
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86 </conditional>
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87 <output name="output1" file="test_output1.vcf" ftype="vcf" />
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88 </test>
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89 <test>
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90 <param name="input1" value="test_input1.vcf" ftype="vcf" />
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91 <param name="filters" value="close_to_indel_filter" />
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92 <conditional name="filter_options">
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93 <param name="show_filter_options" value="yes" />
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94 <param name="indel_window_size" value="5" />
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95 </conditional>
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96 <output name="output1" file="test_output2.vcf" ftype="vcf" />
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97 </test>
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98 <test>
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99 <param name="input1" value="test_input1.vcf" ftype="vcf" />
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100 <param name="filters" value="min_percentage_alt_filter" />
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101 <conditional name="filter_options">
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102 <param name="show_filter_options" value="yes" />
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103 <param name="min_percentage_alt" value="95.0" />
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104 </conditional>
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105 <output name="output1" file="test_output3.vcf" ftype="vcf" />
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106 </test>
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107 <test>
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108 <param name="input1" value="test_input2.vcf" ftype="vcf" />
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109 <param name="filters" value="min_percentage_alt_filter" />
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110 <conditional name="filter_options">
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111 <param name="show_filter_options" value="yes" />
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112 <param name="min_percentage_alt" value="30.0" />
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113 </conditional>
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114 <output name="output1" file="test_output4.vcf" ftype="vcf" />
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115 </test>
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116 <test>
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117 <param name="input1" value="test_input1.vcf" ftype="vcf" />
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118 <param name="filters" value="min_depth_filter" />
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119 <conditional name="filter_options">
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120 <param name="show_filter_options" value="yes" />
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121 <param name="min_depth" value="30" />
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122 </conditional>
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123 <output name="output1" file="test_output5.vcf" ftype="vcf" />
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124 </test>
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125 <test>
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126 <param name="input1" value="test_input1.vcf" ftype="vcf" />
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127 <param name="filters" value="snv_only_filter" />
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128 <output name="output1" file="test_output6.vcf" ftype="vcf" />
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129 </test>
1
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130 <test>
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131 <param name="input1" value="test_input1.vcf" ftype="vcf" />
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132 <param name="filters" value="region_filter" />
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133 <conditional name="filter_options">
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134 <param name="show_filter_options" value="yes" />
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135 <param name="region_filter" value="farhat_rlc" />
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136 </conditional>
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137 <assert_stderr>
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138 <has_text text="masked: 2" />
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139 </assert_stderr>
1
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140 </test>
0
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141 </tests>
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142 <help><![CDATA[
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143 This tool offers multiple options for filtering variants (in
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144 VCF files, relative to M. tuberculosis H37Rv).
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145
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146 It currently has 5 main modes:
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147
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148 1. Filter by region. Mask out variants in certain regions. Region lists available as:
5
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149 1. Refined Low Confidence (RLC) regions from `Marin et al 2022 <https://doi.org/10.1093/bioinformatics/btac023>`_
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150 2. Refined Low Confidence (RLC) and Low Mappability regions from `Marin et al 2022 <https://doi.org/10.1093/bioinformatics/btac023>`_
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151 3. PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_
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152 4. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes
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153 5. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes
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154 6. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome
0
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155 2. Filter by window around indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site.
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156 3. Filter by percentage of alternate allele bases. Mask out variants with less than a minimum percentage (by default 90%) alternative alleles.
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157 4. Filter by depth of aligned reads.
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158 5. Filter out all variants that are not SNV (single nucleotide variants).
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159
5
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160 For region filtering, the default choice is to use the RLC regions. These are based on `Marin et al 2022 <https://doi.org/10.1093/bioinformatics/btac023>`_,
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161 a study of regions of the M. tuberculosis H37Rv genome where Illumina reads don't map well. If you are using reads shower than 100 base pairs
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162 or single-ended reads, you should use the RLC and Low Mappability region filter. The PE/PPE and UVP region filters are retained for backward compatibility
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163 but the afore-mentioned paper has shown that they exclude too much of the genome from analysis.
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164
0
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165 When used together the effects of the filters are added (i.e. a variant is masked out if it is masked by any of the filters).
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166 ]]></help>
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167 <citations>
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168 <citation type="bibtex"><![CDATA[
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169 @misc{vanHeusden2019,
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170 author = {van Heusden, P.},
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171 title = {tb_variant_filter},
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172 year = {2019},
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173 publisher = {GitHub},
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174 journal = {GitHub repository},
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175 howpublished = {\url{https://github.com/pvanheus/tb_variant_filter}},
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176 commit = {4a9b2a4a85ddbfbb0d713a02373c8aa0aa159a6c}
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177 }
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178 ]]></citation>
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179 </citations>
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180 </tool>