| Previous changeset 0:3b1e7c170b10 (2019-10-10) Next changeset 2:e5c84ba20d99 (2021-05-29) |
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Commit message:
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8" |
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modified:
tb_variant_filter.xml |
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| diff -r 3b1e7c170b10 -r eee2da03d1f5 tb_variant_filter.xml --- a/tb_variant_filter.xml Thu Oct 10 17:59:02 2019 -0400 +++ b/tb_variant_filter.xml Sat May 22 10:13:18 2021 +0000 |
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| @@ -1,7 +1,7 @@ -<tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" profile="16.04"> +<tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" profile="21.01"> <description>M. tuberculosis H37Rv VCF filter</description> <macros> - <token name="@TOOL_VERSION@">0.1.3</token> + <token name="@TOOL_VERSION@">0.3.0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">tb_variant_filter</requirement> @@ -57,6 +57,7 @@ <when value="yes"> <param argument="--region_filter" type="select" multiple="true" label="Region filters to enable"> <!-- if these are changed the code above needs to change to keep the defaults in line with those that are default here --> + <option value="farhat_rlc">Refined Low Confidence regions from Farhat lab</option> <option value="pe_ppe" selected="true">PE/PPE</option> <option value="tbprofiler">TBProfiler antibiotic resistant genes</option> <option value="mtbseq">MTBseq antibiotic resistant genes</option> @@ -125,6 +126,17 @@ <param name="filters" value="snv_only_filter" /> <output name="output1" file="test_output6.vcf" ftype="vcf" /> </test> + <test> + <param name="input1" value="test_input1.vcf" ftype="vcf" /> + <param name="filters" value="region_filter" /> + <conditional name="filter_options"> + <param name="show_filter_options" value="yes" /> + <param name="region_filter" value="farhat_rlc" /> + </conditional> + <assert_stderr> + <has_text text="masked: 2" /> + </assert_stdout> + </test> </tests> <help><![CDATA[ This tool offers multiple options for filtering variants (in @@ -133,15 +145,20 @@ It currently has 5 main modes: 1. Filter by region. Mask out variants in certain regions. Region lists available as: - 1. PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_ - 2. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes - 3. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes - 4. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome + 1. Refined Low Confidence (RLC) regions from `Marin et al 2021 <https://www.biorxiv.org/content/10.1101/2021.04.08.438862v1.full>`_ + 2. PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_ + 3. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes + 4. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes + 5. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome 2. Filter by window around indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site. 3. Filter by percentage of alternate allele bases. Mask out variants with less than a minimum percentage (by default 90%) alternative alleles. 4. Filter by depth of aligned reads. 5. Filter out all variants that are not SNV (single nucleotide variants). +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>`_ +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 +review so it is included as an option that is not currently the default. + 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). ]]></help> <citations> |