# HG changeset patch
# User guerler
# Date 1596168850 14400
# Node ID 35dbd62871b02f47343d37ae4aa07b05c8e6c602
# Parent  c3bf37da2daacb487fea93588bb07f3a2935092c
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"

diff -r c3bf37da2daa -r 35dbd62871b0 hhblits.xml
--- a/hhblits.xml	Mon Jul 27 13:29:28 2020 -0400
+++ b/hhblits.xml	Fri Jul 31 00:14:10 2020 -0400
@@ -1,13 +1,14 @@
-<tool id="hhblits" name="HH-blits itererative protein sequence searching" version="0.1.0" python_template_version="3.5">
+<tool id="hhblits" name="HH-blits" version="0.1.0" python_template_version="3.5">
+    <description>itererative protein sequence searching</description>
     <requirements>
         <requirement type="package" version="3.2.0">hhsuite</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        link $hhm_ffdata hhdb_hhm.ffdata &&
-        link $hhm_ffindex hhdb_hhm.ffindex &&
-        link $cs219_ffdata hhdb_cs219.ffdata &&
-        link $cs219_ffindex hhdb_cs219.ffindex &&
-        hhblits -n $n -e $e -i $input -d hhdb -o $output
+        link '$hhm_ffdata' hhdb_hhm.ffdata &&
+        link '$hhm_ffindex' hhdb_hhm.ffindex &&
+        link '$cs219_ffdata' hhdb_cs219.ffdata &&
+        link '$cs219_ffindex' hhdb_cs219.ffindex &&
+        hhblits -n '$n' -e '$e' -i '$input' -d hhdb -o '$output'
     ]]></command>
     <inputs>
         <param format="data" name="input" type="data" label="Query Sequence" help="Single sequence or multiple sequence alignment (MSA)