--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nhmmscan.xml	Tue May 12 15:04:26 2015 -0400
@@ -0,0 +1,101 @@
+<?xml version="1.0"?>
+<tool id="hmmer_nhmmscan" name="nhmmscan" version="@WRAPPER_VERSION@.0">
+  <description>search DNA sequence(s) against a DNA profile database</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+hmmpress $hmmfile;
+
+nhmmscan
+
+@OFORMAT_WITH_OPTS_N@
+@THRESHOLDS_NODOM@
+@CUT@
+@ACCEL_HEUR@
+--B1 $B1
+--B2 $B2
+--B3 $B3
+
+@ADV_OPTS@
+@LENGTHS@
+@CPU@
+@SEED@
+
+$hmmfile
+$seqfile
+> $output
+      ]]></command>
+  <inputs>
+    <expand macro="input_hmm" />
+    <!-- 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"/>
+    <expand macro="thresholds_nodom"/>
+    <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"/>
+
+    <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 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="MADE1.out" lines_diff="120"/>
+      <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"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+nhmmscan is used to search nucleotide sequences against collections of
+nucleotide profiles. For each sequence in <seqfile>, use that query sequence to
+search the target database of profiles in <hmmfile>, and output ranked lists of
+the profiles with the most significant matches to the sequence.
+
+The <seqfile> may contain more than one query sequence. It can be in FASTA
+format, or several other common sequence file formats (genbank, embl, and
+uniprot, among others), or in alignment file formats (stockholm, aligned fasta,
+and others). See the --qformat option for a complete list.
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_N_HELP@
+@THRESHOLDS_NODOM_HELP@
+@CUT_HELP@
+@ACCEL_HEUR_HELP@
+@BIAS_COMP_HELP@
+@ADV_OPTS_HELP@
+@LENGTHS_HELP@
+@SEED_HELP@
+
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation"/>
+</tool>