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comparison tb_variant_filter.xml @ 1:eee2da03d1f5 draft

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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
author iuc
date Sat, 22 May 2021 10:13:18 +0000
parents 3b1e7c170b10
children e5c84ba20d99
comparison
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0:3b1e7c170b10 1:eee2da03d1f5
1 <tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" profile="16.04"> 1 <tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" profile="21.01">
2 <description>M. tuberculosis H37Rv VCF filter</description> 2 <description>M. tuberculosis H37Rv VCF filter</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.1.3</token> 4 <token name="@TOOL_VERSION@">0.3.0</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">tb_variant_filter</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">tb_variant_filter</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
55 <option value="no" selected="true">No</option> 55 <option value="no" selected="true">No</option>
56 </param> 56 </param>
57 <when value="yes"> 57 <when value="yes">
58 <param argument="--region_filter" type="select" multiple="true" label="Region filters to enable"> 58 <param argument="--region_filter" type="select" multiple="true" label="Region filters to enable">
59 <!-- if these are changed the code above needs to change to keep the defaults in line with those that are default here --> 59 <!-- if these are changed the code above needs to change to keep the defaults in line with those that are default here -->
60 <option value="farhat_rlc">Refined Low Confidence regions from Farhat lab</option>
60 <option value="pe_ppe" selected="true">PE/PPE</option> 61 <option value="pe_ppe" selected="true">PE/PPE</option>
61 <option value="tbprofiler">TBProfiler antibiotic resistant genes</option> 62 <option value="tbprofiler">TBProfiler antibiotic resistant genes</option>
62 <option value="mtbseq">MTBseq antibiotic resistant genes</option> 63 <option value="mtbseq">MTBseq antibiotic resistant genes</option>
63 <option value="uvp" selected="true">UVP repeat / insertion sequence sites</option> 64 <option value="uvp" selected="true">UVP repeat / insertion sequence sites</option>
64 </param> 65 </param>
123 <test> 124 <test>
124 <param name="input1" value="test_input1.vcf" ftype="vcf" /> 125 <param name="input1" value="test_input1.vcf" ftype="vcf" />
125 <param name="filters" value="snv_only_filter" /> 126 <param name="filters" value="snv_only_filter" />
126 <output name="output1" file="test_output6.vcf" ftype="vcf" /> 127 <output name="output1" file="test_output6.vcf" ftype="vcf" />
127 </test> 128 </test>
129 <test>
130 <param name="input1" value="test_input1.vcf" ftype="vcf" />
131 <param name="filters" value="region_filter" />
132 <conditional name="filter_options">
133 <param name="show_filter_options" value="yes" />
134 <param name="region_filter" value="farhat_rlc" />
135 </conditional>
136 <assert_stderr>
137 <has_text text="masked: 2" />
138 </assert_stdout>
139 </test>
128 </tests> 140 </tests>
129 <help><![CDATA[ 141 <help><![CDATA[
130 This tool offers multiple options for filtering variants (in 142 This tool offers multiple options for filtering variants (in
131 VCF files, relative to M. tuberculosis H37Rv). 143 VCF files, relative to M. tuberculosis H37Rv).
132 144
133 It currently has 5 main modes: 145 It currently has 5 main modes:
134 146
135 1. Filter by region. Mask out variants in certain regions. Region lists available as: 147 1. Filter by region. Mask out variants in certain regions. Region lists available as:
136 1. PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_ 148 1. Refined Low Confidence (RLC) regions from `Marin et al 2021 <https://www.biorxiv.org/content/10.1101/2021.04.08.438862v1.full>`_
137 2. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes 149 2. PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_
138 3. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes 150 3. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes
139 4. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome 151 4. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes
152 5. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome
140 2. Filter by window around indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site. 153 2. Filter by window around indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site.
141 3. Filter by percentage of alternate allele bases. Mask out variants with less than a minimum percentage (by default 90%) alternative alleles. 154 3. Filter by percentage of alternate allele bases. Mask out variants with less than a minimum percentage (by default 90%) alternative alleles.
142 4. Filter by depth of aligned reads. 155 4. Filter by depth of aligned reads.
143 5. Filter out all variants that are not SNV (single nucleotide variants). 156 5. Filter out all variants that are not SNV (single nucleotide variants).
157
158 For region filtering, the default choice is to use the PE/PPE and UVP regions to mask out variants. `Marin et al 2021 <https://www.biorxiv.org/content/10.1101/2021.04.08.438862v1.full>`_
159 from Prof Maha Farhat's lab make a persuasive argument that their smaller list of Refined Low Confidence (RLC) regions is a better argument but this work has not yet been peer
160 review so it is included as an option that is not currently the default.
144 161
145 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). 162 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).
146 ]]></help> 163 ]]></help>
147 <citations> 164 <citations>
148 <citation type="bibtex"><![CDATA[ 165 <citation type="bibtex"><![CDATA[