# HG changeset patch
# User iuc
# Date 1632421125 0
# Node ID 67af24676bd63e9e6e90d462aca34b353bd03449
# Parent  095162ba8e90d1d85684ae4c6cd0fce6a172c246
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 8913264abbcee238b5ef81268d111db98c942bfe"

diff -r 095162ba8e90 -r 67af24676bd6 feelnc_wrapper.xml
--- a/feelnc_wrapper.xml	Tue Dec 01 10:55:23 2020 +0000
+++ b/feelnc_wrapper.xml	Thu Sep 23 18:18:45 2021 +0000
@@ -1,16 +1,20 @@
 <?xml version="1.0" encoding="utf-8"?>
 <tool id="feelnc" name="FEELnc" profile="17.01" version="0.2">
     <description>FlExible Extraction of LncRNA</description>
+    <xrefs>
+        <xref type="bio.tools">feelnc</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="0.2">feelnc</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 export FEELNCPATH=\$(dirname \$(command -v FEELnc_pipeline.sh))/../ &&
-
+## Symlink the genome FASTA to the working directory to avoid writing .index to inputdir
+ln -s '$genome' genome_fa &&
 FEELnc_pipeline.sh
 --candidate='${candidate}'
 --reference='${reference}'
---genome='${genome}'
+--genome=genome_fa
 --outname='candidate_lncRNA'
 --outdir='out_feelnc'