Mercurial > repos > iuc > tb_variant_filter
comparison tb_variant_filter.xml @ 5:ee4a90760848 draft
planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit e064fb07acad057d3df849a6f153ed6ef90837f1
author | iuc |
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date | Sun, 18 Dec 2022 17:39:30 +0000 |
parents | e7aff4a85df5 |
children | 32f14a2723ec |
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4:e7aff4a85df5 | 5:ee4a90760848 |
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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 < 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[ |