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comparison tb_variant_filter.xml @ 6:32f14a2723ec draft default tip

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planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 8ef8941514b1a99b5608c41c0b3caa2ea4b54ac1
author iuc
date Mon, 14 Aug 2023 09:47:13 +0000
parents ee4a90760848
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5:ee4a90760848 6:32f14a2723ec
1 <tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" 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@">0.3.6</token> 4 <token name="@TOOL_VERSION@">0.4.0</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[
146 It currently has 5 main modes: 146 It currently has 5 main modes:
147 147
148 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:
149 1. Refined Low Confidence (RLC) regions from `Marin et al 2022 <https://doi.org/10.1093/bioinformatics/btac023>`_ 149 1. Refined Low Confidence (RLC) regions from `Marin et al 2022 <https://doi.org/10.1093/bioinformatics/btac023>`_
150 2. Refined Low Confidence (RLC) and Low Mappability regions from `Marin et al 2022 <https://doi.org/10.1093/bioinformatics/btac023>`_ 150 2. Refined Low Confidence (RLC) and Low Mappability regions from `Marin et al 2022 <https://doi.org/10.1093/bioinformatics/btac023>`_
151 3. PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_ 151 3. PE/PPE genes from `Fishbein et al 2015 <https://web.archive.org/web/20210929032252/https://onlinelibrary.wiley.com/doi/10.1111/mmi.12981>`_
152 4. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes 152 4. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes
153 5. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes 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 154 6. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome
155 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.
156 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.