# HG changeset patch
# User iuc
# Date 1633521942 0
# Node ID 53ce8be43212f1b440bebe7fa8e3e87904c54eb1
# Parent  1cea2358365556c240ba2db4d492235b91cdd576
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 commit a786695a05177842dcc89ef6bb21b38d7e7ce2db"

diff -r 1cea23583655 -r 53ce8be43212 gatk4_Mutect2.xml
--- a/gatk4_Mutect2.xml	Fri Aug 14 04:55:49 2020 -0400
+++ b/gatk4_Mutect2.xml	Wed Oct 06 12:05:42 2021 +0000
@@ -699,14 +699,11 @@
 somatic genotyping engine of the original MuTect (`Cibulskis et al.,
 2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__)
 with the assembly-based machinery of
-`HaplotypeCaller <https://www.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php>`__.
+`HaplotypeCaller <https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__.
 
 This tool is featured in the *Somatic Short Mutation calling Best
-Practice Workflow*. See
-`Tutorial#11136 <https://software.broadinstitute.org/gatk/documentation/article?id=11136>`__
-for a step-by-step description of the workflow and
-`Article#11127 <https://software.broadinstitute.org/gatk/documentation/article?id=11127>`__
-for an overview of what traditional somatic calling entails. For the
+Practice Workflow*. See `this article <https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__
+for an overview of what traditional somatic calling entails, with usage examples. For the
 latest pipeline scripts, see the `Mutect2 WDL scripts
 directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__.
 Although we present the tool for somatic calling, it may apply to other
diff -r 1cea23583655 -r 53ce8be43212 macros.xml
--- a/macros.xml	Fri Aug 14 04:55:49 2020 -0400
+++ b/macros.xml	Wed Oct 06 12:05:42 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@VERSION@">4.1.7.0</token>
-    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy0</token>
+    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</token>
 
     <xml name="requirements">
         <requirements>