# HG changeset patch
# User iuc
# Date 1586542255 14400
# Node ID 3be27a9a7313b0eca775970c1d21b8973338d064
# Parent  fd2d6e035c3f3d734857c5cb7c4e280a38483953
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 093a027ca9e7d34e7d12cd14ca0d0dacadfcb78b"

diff -r fd2d6e035c3f -r 3be27a9a7313 gatk4_Mutect2.xml
--- a/gatk4_Mutect2.xml	Mon Nov 18 13:45:47 2019 -0500
+++ b/gatk4_Mutect2.xml	Fri Apr 10 14:10:55 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@1" profile="18.05">
+<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@2" profile="18.05">
     <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>
     <macros>
         <import>macros.xml</import>
@@ -38,8 +38,8 @@
             #end if
         #end if
 
-        @CMD_BEGIN@ GetSampleName --input="input.bam" --output="samplename.txt" &&
-        sample=`cat samplename.txt` &&
+        gatk GetSampleName --input="input.bam" --output="samplename.txt" &&
+        sample=`cat samplename.txt | sed 's/"//g'` &&
 
         #if str($optional.optional_parameters) == 'yes'
             #if $optional.panel_of_normals
@@ -76,7 +76,7 @@
 
         #end if
 
-        @CMD_BEGIN@ Mutect2 --QUIET $ref_flag --tumor-sample \$sample
+        gatk Mutect2 --QUIET $ref_flag --tumor-sample "\$sample"
 
         #include source=$gatk_bam_input#
 
@@ -770,4 +770,4 @@
     <citations>
         <expand macro="citations"/>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
diff -r fd2d6e035c3f -r 3be27a9a7313 macros.xml
--- a/macros.xml	Mon Nov 18 13:45:47 2019 -0500
+++ b/macros.xml	Fri Apr 10 14:10:55 2020 -0400
@@ -17,9 +17,6 @@
         <version_command>gatk SortSam --version 2>&amp;1 | grep Version | cut -d ':' -f 2</version_command>
     </xml>
 
-    <!--Command token, java options should not be hard coded here.-->
-    <token name="@CMD_BEGIN@">[[ -z \$_JAVA_OPTIONS ]] &amp;&amp; export JAVA_OPTS=\$_JAVA_OPTIONS &amp;&amp; gatk</token>
-
     <!--Define sections that parameters could exist within.-->
     <template name="set_sections">
         #set global $sections = ['', 'optional.', 'advanced.', 'deprecated.']