--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmalign.xml	Tue May 12 15:04:26 2015 -0400
@@ -0,0 +1,65 @@
+<?xml version="1.0"?>
+<tool id="hmmer_hmmalign" name="hmmalign" version="@WRAPPER_VERSION@.0">
+  <description>align sequences to a profile HMM</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+hmmalign
+
+$trim
+@FORMAT_SELECTOR@
+--outformat stockholm
+
+$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=""/>
+    <expand macro="format_selector"/>
+  </inputs>
+  <outputs>
+    <data format="stockholm" name="output" label="Alignment of $seq.name to $hmmfile.name">
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="hmmfile" value="globins4.hmm"/>
+      <param name="seq" value="globins45.fa"/>
+      <output name="output" file="globins-45-align.sto" lines_diff="20"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+Perform a multiple sequence alignment of all the sequences in <seqfile> by
+aligning them individually to the profile HMM in <hmmfile>. The new alignment
+is output to stdout in Stockholm format.  The <hmmfile> should contain only a
+single profile. If it contains more, only the first profile in the file will be
+used.
+
+Either <hmmfile> or <seqfile> (but not both) may be ’-’ (dash), which means
+reading this input from stdin rather than a file.
+
+The sequences in <seqfile> are aligned in unihit local alignment mode.
+Therefore they should already be known to contain only a single domain (or a
+fragment of one). The optimal alignment may assign some residues as
+nonhomologous (N and C states), in which case these residues are still included
+in the resulting alignment, but shoved to the outer edges. To trim these
+unaligned nonhomologous residues from the result, see the --trim option.
+
+
+@HELP_PRE_OTH@
+
+@FORMAT_SELECTOR_HELP@
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation"/>
+</tool>