--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/emboss_5/emboss_patmatdb.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,49 @@
+<tool id="EMBOSS: patmatdb67" name="patmatdb" version="5.0.0">
+  <description>Search a protein sequence with a motif</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>patmatdb -sequence $input1 -outfile $out_file1 -motif "$motif" -rformat3 $out_format1 -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Main sequence</label>
+    </param>
+    <param name="motif" size="4" type="text" value="">
+      <label>Motif to search for</label>
+    </param>
+    <param name="out_format1" type="select">
+      <label>Output Report File Format</label>
+      <option value="dbmotif">DbMotif</option>
+      <option value="embl">EMBL</option>
+      <option value="genbank">GENBANK</option>
+      <option value="gff">GFF</option>
+      <option value="pir">PIR</option>
+      <option value="swiss">SwissProt</option>
+      <option value="diffseq">Diffseq</option>
+      <option value="excel">Excel (tab delimited)</option>
+      <option value="feattable">FeatTable</option>
+      <option value="motif">Motif</option>
+      <option value="regions">Regions</option>
+      <option value="seqtable">SeqTable</option>
+      <option value="simple">SRS Simple</option>
+      <option value="srs">SRS</option>
+      <option value="table">Table</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="dbmotif" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="motif" value="aa"/>
+      <param name="out_format1" value="excel"/>
+      <output name="out_file1" file="emboss_patmatdb_out.tabular"/>
+    </test>
+  </tests>
+  <code file="emboss_format_corrector.py" />
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/patmatdb.html
+  </help>
+</tool>
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