Mercurial > repos > iuc > tetyper

changeset 2:edcf603bedfd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit a5b87b732eb5016450c39c07be4f5de95ff81fc7"
author iuc
date Tue, 16 Nov 2021 19:57:38 +0000
parents 36093854bfc7
children 2b21643ce8d7
files tetyper.xml
diffstat 1 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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}'