--- a/hmmalign.xml	Wed Apr 04 13:59:49 2018 -0400
+++ b/hmmalign.xml	Sat Apr 07 03:48:42 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hmmer_hmmalign" name="hmmalign" version="@WRAPPER_VERSION@.0">
+<tool id="hmmer_hmmalign" name="hmmalign" version="@TOOL_VERSION@">
   <description>align sequences to a profile HMM</description>
   <macros>
     <import>macros.xml</import>
@@ -13,20 +13,19 @@
 @FORMAT_SELECTOR@
 --outformat stockholm
 
-$hmmfile
-$seq
-> $output
-      ]]></command>
+'$hmmfile'
+'$seq'
+> '$output'
+  ]]></command>
   <inputs>
     <param name="seq" type="data" format="fasta" label="Sequence to align against model" help="Sequence should be in FASTA format"/>
     <expand macro="input_hmm" />
     <!-- TODO: mapali -->
-    <param name="trim" type="boolean" truevalue="--trim" label="trim terminal tails of nonaligned residues from alignment" help="(--trim)" falsevalue=""/>
+    <param argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="trim terminal tails of nonaligned residues from alignment" />
     <expand macro="format_selector"/>
   </inputs>
   <outputs>
-    <data format="stockholm" name="output" label="Alignment of $seq.name to $hmmfile.name">
-    </data>
+    <data name="output" format="stockholm" label="Alignment of $seq.name to $hmmfile.name" />
   </outputs>
   <tests>
     <test>
@@ -60,6 +59,6 @@
 @FORMAT_SELECTOR_HELP@
 
 @ATTRIBUTION@
-]]></help>
+  ]]></help>
   <expand macro="citation"/>
 </tool>