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+++ b/mugsy.xml	Fri Sep 06 05:58:59 2013 -0400
@@ -0,0 +1,44 @@
+<tool id="mugsy" name="Mugsy" version="1.0.1">
+  <description>multiple whole genome aligner</description>
+  <requirements>
+    <requirement type="package" version="1.2.3.1">mugsy</requirement>
+  </requirements>
+  <command interpreter="python">
+    mugsy.py -r $reference -c $contigs -l $logfile --ml $mugsylog --maf $maffile
+  </command>
+
+  <inputs>
+    <param name="reference" type="data" format="fasta" label="Reference" help="FASTA format" />
+    <param name="contigs" type="data" format="fasta" label="Contigs/draft" help="FASTA format" />
+  </inputs>
+  <outputs>
+    <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
+    <data name="mugsylog" format="txt" label="${tool.name} on ${on_string}: mugsy.log" />
+    <data name="maffile" format="maf" label="${tool.name} on ${on_string}: MAF" />
+  </outputs>
+  <tests>
+
+  </tests>
+  <help>
+**What it does**
+
+Mugsy generates a MAF (multiple alignment format) file containing the multiple alignments from FASTA inputs.
+
+This implementation runs with two files only: reference vs contigs/draft(s). For multiple alignment a single Multi-FASTA file containing all contigs should be provided.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
+
+.. _CRS4 Srl.: http://www.crs4.it/
+.. _MIT license: http://opensource.org/licenses/MIT
+
+If you use this tool in Galaxy, please cite the website http://orione.crs4.it/
+
+This tool uses `Mugsy`_, which is licensed separately. Please cite |Angiuoli2010|_.
+
+.. _Mugsy: http://mugsy.sourceforge.net/
+.. |Angiuoli2010| replace:: Angiuoli, S. V., Salzberg S. L. (2010) Mugsy: Fast multiple alignment of closely related whole genomes. *Bioinformatics* 27(3), 334-342
+.. _Angiuoli2010: http://bioinformatics.oxfordjournals.org/content/27/3/334
+  </help>
+</tool>