Mercurial > repos > dfornika > gatk4

changeset 9:df3ef6a4ed45 draft default tip

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planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/gatk4 commit 54c5ec0b3958115ccb9071184268bfe4f7425baa-dirty
author dfornika
date Mon, 14 Jan 2019 20:18:04 -0500
parents a4c61d0d9938
children
files gatk4_HaplotypeCaller.xml
diffstat 1 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/gatk4_HaplotypeCaller.xml	Mon Jan 14 14:18:11 2019 -0500
+++ b/gatk4_HaplotypeCaller.xml	Mon Jan 14 20:18:04 2019 -0500
@@ -16,10 +16,10 @@
       samtools index input.bam &&
       ln -s '$reference' reference.fasta &&
       samtools faidx reference.fasta &&
-      picard CreateSequenceDictionary REFERENCE=reference.fasta &&
       gatk HaplotypeCaller
         --input input.bam
         --reference reference.fasta
+	--sequence-dictionary '$sequence_dictionary'
 	--sample-ploidy '$ploidy'
         --output '$output'
     ]]>
@@ -27,6 +27,7 @@
   <inputs>
     <param name="input" type="data" format="sam,bam" />
     <param name="reference" type="data" format="fasta,fa" />
+    <param name="sequence_dictionary" type="data" />
     <param name="ploidy" type="integer" value="1" min="1" />
   </inputs>
   <outputs>