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comparison 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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4:e7aff4a85df5 5:ee4a90760848
1 <tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy2" profile="20.09"> 1 <tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" profile="20.09">
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@">0.3.5</token> 4 <token name="@TOOL_VERSION@">0.3.6</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[
10 tb_variant_filter 10 tb_variant_filter
11 #if "region_filter" in str($filters).split(',') 11 #if "region_filter" in str($filters).split(',')
12 #if str($filter_options.show_filter_options) == "yes": 12 #if str($filter_options.show_filter_options) == "yes":
13 --region_filter $filter_options.region_filter 13 --region_filter $filter_options.region_filter
14 #else 14 #else
15 --region_filter pe_ppe,uvp 15 --region_filter farhat_rlc
16 #end if 16 #end if
17 #end if 17 #end if
18 #if "close_to_indel_filter" in str($filters).split(',') 18 #if "close_to_indel_filter" in str($filters).split(',')
19 --close_to_indel_filter 19 --close_to_indel_filter
20 #if str($filter_options.show_filter_options) == "yes": 20 #if str($filter_options.show_filter_options) == "yes":
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="farhat_rlc" selected="true">Refined Low Confidence regions from Farhat lab</option>
61 <option value="pe_ppe" selected="true">PE/PPE</option> 61 <option value="farhat_rlc_lowmap">Refined Low Confidence and Low Mappability regions from Farhat lab (for &lt; 100bp or single ended reads)</option>
62 <option value="pe_ppe">PE/PPE</option>
62 <option value="tbprofiler">TBProfiler antibiotic resistant genes</option> 63 <option value="tbprofiler">TBProfiler antibiotic resistant genes</option>
63 <option value="mtbseq">MTBseq antibiotic resistant genes</option> 64 <option value="mtbseq">MTBseq antibiotic resistant genes</option>
64 <option value="uvp" selected="true">UVP repeat / insertion sequence sites</option> 65 <option value="uvp">UVP repeat / insertion sequence sites</option>
65 </param> 66 </param>
66 <param argument="--indel_window_size" type="integer" value="5" label="Window to mask around indels"/> 67 <param argument="--indel_window_size" type="integer" value="5" label="Window to mask around indels"/>
67 <param argument="--min_percentage_alt" type="float" value="90" 68 <param argument="--min_percentage_alt" type="float" value="90"
68 label="Minimum alternate allele percentage to accept"/> 69 label="Minimum alternate allele percentage to accept"/>
69 <param argument="--min_depth" type="integer" value="30" label="Minimum read depth (coverage)"/> 70 <param argument="--min_depth" type="integer" value="30" label="Minimum read depth (coverage)"/>
143 VCF files, relative to M. tuberculosis H37Rv). 144 VCF files, relative to M. tuberculosis H37Rv).
144 145
145 It currently has 5 main modes: 146 It currently has 5 main modes:
146 147
147 1. Filter by region. Mask out variants in certain regions. Region lists available as: 148 1. Filter by region. Mask out variants in certain regions. Region lists available as:
148 1. Refined Low Confidence (RLC) regions from `Marin et al 2021 <https://www.biorxiv.org/content/10.1101/2021.04.08.438862v1.full>`_ 149 1. Refined Low Confidence (RLC) regions from `Marin et al 2022 <https://doi.org/10.1093/bioinformatics/btac023>`_
149 2. PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_ 150 2. Refined Low Confidence (RLC) and Low Mappability regions from `Marin et al 2022 <https://doi.org/10.1093/bioinformatics/btac023>`_
150 3. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes 151 3. PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_
151 4. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes 152 4. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes
152 5. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome 153 5. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes
154 6. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome
153 2. Filter by window around indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site. 155 2. Filter by window around indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site.
154 3. Filter by percentage of alternate allele bases. Mask out variants with less than a minimum percentage (by default 90%) alternative alleles. 156 3. Filter by percentage of alternate allele bases. Mask out variants with less than a minimum percentage (by default 90%) alternative alleles.
155 4. Filter by depth of aligned reads. 157 4. Filter by depth of aligned reads.
156 5. Filter out all variants that are not SNV (single nucleotide variants). 158 5. Filter out all variants that are not SNV (single nucleotide variants).
157 159
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>`_ 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>`_,
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 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
160 review so it is included as an option that is not currently the default. 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
163 but the afore-mentioned paper has shown that they exclude too much of the genome from analysis.
161 164
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). 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).
163 ]]></help> 166 ]]></help>
164 <citations> 167 <citations>
165 <citation type="bibtex"><![CDATA[ 168 <citation type="bibtex"><![CDATA[