# HG changeset patch
# User iuc
# Date 1655970197 0
# Node ID 0e85267c5167549c4dd7dd7d75256196508f0cdc
# Parent  d465ebeb058ff8fdebfb3a31076c76ce45f024c9
planemo upload commit c95f14a2264c02a4d9ff1f629a450ba2ea73b109

diff -r d465ebeb058f -r 0e85267c5167 barrnap.xml
--- a/barrnap.xml	Mon Aug 30 21:46:12 2021 +0000
+++ b/barrnap.xml	Thu Jun 23 07:43:17 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="barrnap" name="barrnap" version="1.2.1">
+<tool id="barrnap" name="barrnap" version="1.2.2">
     <description>Locate ribosomal RNA's in a fasta file. (GFF output)</description>
    <xrefs>
         <xref type="bio.tools">barrnap</xref>
@@ -8,6 +8,9 @@
     </requirements>
     <version_command>barrnap --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
+        ## symlink fasta because tool generates .fai
+        ln -s '$fasta_file' query.fa &&
+
         barrnap
         --quiet
         --threads \${GALAXY_SLOTS:-1}
@@ -21,7 +24,7 @@
             --outseq '$fasta_out'
         #end if
         --kingdom $kingdom
-        '$fasta_file'
+        query.fa
         > '$gff'
     ]]>
     </command>