# HG changeset patch
# User iuc
# Date 1692006433 0
# Node ID 32f14a2723ec529f1050d104d310fbf574683731
# Parent  ee4a907608481f48cdd41980fbdad61a1bbdc5f9
planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 8ef8941514b1a99b5608c41c0b3caa2ea4b54ac1

diff -r ee4a90760848 -r 32f14a2723ec tb_variant_filter.xml
--- a/tb_variant_filter.xml	Sun Dec 18 17:39:30 2022 +0000
+++ b/tb_variant_filter.xml	Mon Aug 14 09:47:13 2023 +0000
@@ -1,7 +1,7 @@
 <tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" profile="20.09">
     <description>M. tuberculosis H37Rv VCF filter</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.3.6</token>
+        <token name="@TOOL_VERSION@">0.4.0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">tb_variant_filter</requirement>
@@ -148,7 +148,7 @@
 1. Filter by region. Mask out variants in certain regions. Region lists available as:
     1.  Refined Low Confidence (RLC) regions from `Marin et al 2022 <https://doi.org/10.1093/bioinformatics/btac023>`_
     2.  Refined Low Confidence (RLC) and Low Mappability regions from `Marin et al 2022 <https://doi.org/10.1093/bioinformatics/btac023>`_
-    3.  PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_
+    3.  PE/PPE genes from `Fishbein et al 2015 <https://web.archive.org/web/20210929032252/https://onlinelibrary.wiley.com/doi/10.1111/mmi.12981>`_
     4. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes
     5. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes
     6. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome