--- a/nhmmscan.xml	Mon Nov 14 15:12:05 2016 -0500
+++ b/nhmmscan.xml	Sat Apr 07 03:49:11 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hmmer_nhmmscan" name="nhmmscan" version="@WRAPPER_VERSION@.0">
+<tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@">
   <description>search DNA sequence(s) against a DNA profile database</description>
   <macros>
     <import>macros.xml</import>
@@ -7,8 +7,7 @@
   <expand macro="requirements"/>
   <expand macro="stdio"/>
   <command><![CDATA[
-hmmpress $hmmfile;
-
+@INPUTHMMCHOICE@
 nhmmscan
 
 @OFORMAT_WITH_OPTS_N@
@@ -24,12 +23,12 @@
 @CPU@
 @SEED@
 
-$hmmfile
-$seqfile
-> $output
-      ]]></command>
+'$input_hmm_filename'
+'$seqfile'
+> '$output'
+  ]]></command>
   <inputs>
-    <expand macro="input_hmm" />
+    <expand macro="input_hmm_choice" />
     <!-- todo use Galaxy features like data libraries/data tables/??? -->
     <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
     <expand macro="oformat_with_opts_n"/>
@@ -37,37 +36,38 @@
     <expand macro="cut"/>
     <expand macro="accel_heur_xml"/>
 
-    <param name="B1" type="integer" label="window length for biased-composition modifier (MSV)" help="(--B1)" value="110"/>
-    <param name="B2" type="integer" label="window length for biased-composition modifier (Vit)" help="(--B2)" value="240"/>
-    <param name="B3" type="integer" label="window length for biased-composition modifier (Fwd)" help="(--B3)" value="1000"/>
+    <param argument="--B1" type="integer" value="110" label="window length for biased-composition modifier (MSV)" />
+    <param argument="--B2" type="integer" value="240" label="window length for biased-composition modifier (Vit)" />
+    <param argument="--B3" type="integer" value="1000" label="window length for biased-composition modifier (Fwd)" />
 
     <expand macro="adv_opts"/>
     <expand macro="lengths"/>
     <expand macro="seed"/>
   </inputs>
   <outputs>
-    <data format="txt" name="output" label="HMM matches of $seqfile.name in $hmmfile.name"/>
+    <data name="output" format="txt" label="HMM matches of $seqfile.name against the profile database"/>
 
-    <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name">
-      <filter>'tblout' in str(oformat)</filter>
+    <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database">
+      <filter>oformat and 'tblout' in oformat</filter>
     </data>
-    <data format="txt" name="dfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
-      <filter>'pfamtblout' in str(oformat)</filter>
+    <data name="dfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database">
+      <filter>oformat and 'dfamtblout' in oformat</filter>
     </data>
-    <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name">
-      <filter>'aliscoresout' in str(oformat)</filter>
+    <data name="aliscoresout" format="txt" label="Scores for positional matches of $seqfile.name against the profile database">
+      <filter>oformat and 'aliscoresout' in oformat</filter>
     </data>
   </outputs>
   <tests>
     <test>
-      <param name="hmmfile" value="MADE1.hmm"/>
+      <param name="input_hmm_conditional|input_hmm_source" value="history"/>
+      <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
       <param name="seqfile" value="dna_target.fa"/>
       <expand macro="oformat_test" />
       <expand macro="seed_test" />
-      <output name="output" file="MADE1.out" lines_diff="140"/>
-      <output name="tblout" file="MADE1.out.tblout" lines_diff="30"/>
-      <output name="domtblout" file="MADE1.out.domtblout" lines_diff="30"/>
-      <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="36"/>
+      <output name="output" file="MADE1.nhmmscan_out" lines_diff="12" />
+      <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10" />
+      <output name="dfamtblout" file="MADE1.nhmmscan_out.dfamtblout" />
+      <output name="aliscoresout" file="MADE1.nhmmscan_out.aliscoresout" lines_diff="10" />
     </test>
   </tests>
   <help><![CDATA[