--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmscan.xml	Sat Jun 25 15:06:16 2016 -0400
@@ -0,0 +1,84 @@
+<?xml version="1.0"?>
+<tool id="hmmer_hmmscan" name="hmmscan" version="@WRAPPER_VERSION@.0">
+  <description>search sequence(s) against a profile database</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+## "Press" database
+hmmpress $hmmfile;
+## Scan
+hmmscan
+
+@OFORMAT_WITH_OPTS@
+@THRESHOLDS@
+@CUT@
+@ACCEL_HEUR@
+@ADV_OPTS@
+@CPU@
+@SEED@
+
+$hmmfile
+$seqfile
+> $output;
+## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype
+rm ${hmmfile}.h3m ${hmmfile}.h3i ${hmmfile}.h3f ${hmmfile}.h3p;
+      ]]></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"/>
+    <expand macro="thresholds_xml"/>
+    <expand macro="cut"/>
+    <expand macro="accel_heur_xml"/>
+    <expand macro="adv_opts"/>
+    <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 oformat</filter>
+    </data>
+    <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
+      <filter>'domtblout' in oformat</filter>
+    </data>
+    <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
+      <filter>'pfamtblout' in 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="24"/>
+      <output name="tblout" file="MADE1.out.tblout" lines_diff="20"/>
+      <output name="domtblout" file="MADE1.out.domtblout" lines_diff="20"/>
+      <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="20"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+hmmscan is used to search protein sequences against collections of protein
+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.
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_HELP@
+@THRESHOLDS_HELP@
+@CUT_HELP@
+@ACCEL_HEUR_HELP@
+@ADV_OPTS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation"/>
+</tool>