--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nhmmer.xml	Sat Jun 25 15:07:17 2016 -0400
@@ -0,0 +1,90 @@
+<?xml version="1.0"?>
+<tool id="hmmer_nhmmer" name="nhmmer" version="@WRAPPER_VERSION@.0">
+  <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+nhmmer
+
+@OFORMAT_WITH_OPTS_N@
+@HSSI@
+@THRESHOLDS_NODOM@
+@CUT@
+@ACCEL_HEUR@
+@FORMAT_SELECTOR@
+@ADV_OPTS@
+@LENGTHS@
+@CPU@
+@SEED@
+
+$hmmfile
+$seqfile
+> $output
+      ]]></command>
+  <inputs>
+    <expand macro="input_hmm" />
+    <param name="seqfile" type="data" format="fasta" label="Target sequence file"/>
+    <expand macro="oformat_with_opts_n"/>
+    <expand macro="hssi"/>
+    <expand macro="thresholds_nodom"/>
+    <expand macro="cut" />
+    <expand macro="accel_heur_xml"/>
+    <expand macro="format_selector_noprot"/>
+    <expand macro="adv_opts"/>
+    <expand macro="lengths"/>
+    <!-- TODO: block_length toponly bottomonly -->
+    <expand macro="seed"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" label="NHMMER search of $seqfile.name in $hmmfile.name"/>
+
+    <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>
+    <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>
+    <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name">
+      <filter>'aliscoresout' in str(oformat)</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="hmmfile" value="MADE1.hmm"/>
+      <param name="seqfile" value="dna_target.fa"/>
+      <expand macro="oformat_test" />
+      <expand macro="seed_test" />
+      <output name="output" file="nhmmer.out" lines_diff="32"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+nhmmer is used to search one or more nucleotide queries against a nucleotide
+sequence database. For each query in <queryfile>, use that query to search the
+target database of sequences in <seqdb>, and output a ranked list of the hits
+with the most significant matches to the query. A query may be either a profile
+model built using hmmbuild, a sequence alignment, or a single sequence.
+Sequence based queries can be in a number of formats (see --qformat), and can
+typically be autodetected. Note that only Stockholm format supports the use of
+multiple sequence-based queries.
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_N_HELP@
+@HSSI_HELP@
+@THRESHOLDS_NODOM_HELP@
+@CUT_HELP@
+@ACCEL_HEUR_HELP@
+@FORMAT_SELECTOR_HELP@
+@ADV_OPTS_HELP@
+@LENGTHS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation"/>
+</tool>