# HG changeset patch
# User iuc
# Date 1637092658 0
# Node ID edcf603bedfd47eb8a6baf33b94ffc4cd269c993
# Parent  36093854bfc72e8e682f6ba49e503e54986f63a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit a5b87b732eb5016450c39c07be4f5de95ff81fc7"

diff -r 36093854bfc7 -r edcf603bedfd tetyper.xml
--- a/tetyper.xml	Sat Jan 18 15:04:39 2020 -0500
+++ b/tetyper.xml	Tue Nov 16 19:57:38 2021 +0000
@@ -8,6 +8,8 @@
     </requirements>
     <command detect_errors="exit_code">
         <![CDATA[
+        ## avoid creating indices in the inputdir
+        ln -s '$reference' reference.fa &&
         TETyper.py
             --threads \${GALAXY_SLOTS:-1}
             #if $collection_paired.selector == "paired"
@@ -15,7 +17,7 @@
             #elif $collection_paired.selector == "collection":
                 --fq1 '${collection_paired.input_pair.forward}' --fq2 '${collection_paired.input_pair.reverse}'
             #end if
-            --ref '${reference}'
+            --ref 'reference.fa'
             --flank_len '${flank_length}'
             --min_reads '${min_reads}'
             --min_each_strand '${min_each_strand}'