| Previous changeset 4:1cea23583655 (2020-08-14) Next changeset 6:fb0bb7174530 (2022-08-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 commit a786695a05177842dcc89ef6bb21b38d7e7ce2db" |
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modified:
gatk4_Mutect2.xml macros.xml |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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> |