--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/emboss_5/emboss_matcher.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,57 @@
+<tool id="EMBOSS: matcher52" name="matcher" version="5.0.0">
+  <description>Finds the best local alignments between two sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence 1</label>
+    </param>
+    <param format="data" name="input2" type="data">
+      <label>Sequence 2</label>
+    </param>
+    <param name="alternatives" size="4" type="text" value="1">
+      <label>Number of alternative matches</label>
+    </param>
+    <param name="gapopen" size="4" type="text" value="16">
+      <label>Gap penalty</label>
+    </param>
+    <param name="gapextend" size="4" type="text" value="4">
+      <label>Gap length (extension) penalty</label>
+    </param>
+    <param name="out_format1" type="select">
+      <label>Output Alignment File Format</label>
+      <option value="markx0">Markx0 (p)</option>
+      <option value="simple">Simple (m)</option>
+      <option value="fasta">FASTA (m)</option>
+      <option value="msf">MSF (m)</option>
+      <option value="srs">SRS (m)</option>
+      <option value="pair">Pair (p)</option>
+      <option value="markx1">Markx1 (p)</option>
+      <option value="markx2">Markx2 (p)</option>
+      <option value="markx3">Markx3 (p)</option>
+      <option value="markx10">Markx10 (p)</option>
+      <option value="srspair">SRS pair (p)</option>
+      <option value="score">Score (p)</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="markx0" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="input2" value="1.fasta"/>
+      <param name="alternatives" value="1"/>
+      <param name="gapopen" value="16"/>
+      <param name="gapextend" value="4"/>
+      <param name="out_format1" value="fasta"/>
+      <output name="out_file1" file="emboss_matcher_out.fasta"/>
+    </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/matcher.html
+  </help>
+</tool>
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