Mercurial > repos > iuc > tetyper

diff tetyper.xml @ 2:287335d65198 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit a5b87b732eb5016450c39c07be4f5de95ff81fc7"
author: iuc
date: Tue, 16 Nov 2021 19:57:10 +0000
parents: ea4310309d66
children: 2ccf19849796
--- a/tetyper.xml	Sat Jan 18 20:04:16 2020 +0000
+++ b/tetyper.xml	Tue Nov 16 19:57:10 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}'