Mercurial > repos > iuc > gatk4_mutect2

diff gatk4_Mutect2.xml @ 2:3be27a9a7313 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 093a027ca9e7d34e7d12cd14ca0d0dacadfcb78b"
author iuc
date Fri, 10 Apr 2020 14:10:55 -0400
parents fd2d6e035c3f
children 287c4af133e6
line wrap: on
line diff
--- 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>