--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MUMmer/mummer_tool.xml	Tue Mar 31 14:19:49 2015 +0200
@@ -0,0 +1,114 @@
+<tool id="mummer_tool" name="MUMmer compare and plot" version="0.4.alx" force_history_refresh="True">
+  <description>: Compare and plot genomes (Nucmer or Promer)</description>
+  <command interpreter="bash">
+  		mummer_tool.sh
+		$input_ref $input_query
+		$out_delta $out_coords $out_png $out_log
+		$algorithm
+		$keep_delta $make_coords $keep_log $make_image
+		$cmd_extra
+  </command>
+	<inputs>
+		<param name="algorithm" type="select" format="text" value="nucmer" label="Algorithm" help="Nucmer dna or Promer protein (FASTA: protein. Dna is six frame translated)">
+			<option value="nucmer">Nucmer DNA</option>
+			<option value="promer">Promer</option>
+		</param>
+		<param name="input_ref" type="data" format="fasta" label="Reference sequence" />
+		<param name="input_query" type="data" format="fasta" label="Sequence query file"/>
+		<param name="make_image" type="select" format="text" value="yes" label="Generate MUMmerplot" help="MUMmerplot will be run with default settings and --large --png as fixed image.">
+			<option value="yes">Yes</option>
+			<option value="no">No</option>
+		</param>
+		<param name="keep_delta" type="select" format="text" value="no" label="Keep delta file" help="i.e. for further processing">
+			<option value="no">No</option>
+			<option value="yes">Yes</option>
+		</param>
+		<param name="make_coords" type="select" format="text" value="yes" label="Make coords file" help="Uses the -r argument to sort lines by reference.">
+			<option value="no">No</option>
+			<option value="yes">Yes</option>
+		</param>
+		<param name="keep_log" type="select" format="text" value="no" label="Keep console log file" help="i.e. for debugging">
+			<option value="no">No</option>
+			<option value="yes">Yes</option>
+		</param>
+		<param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="the --coords is run by default" />
+	</inputs>
+	<outputs>
+		<data name="out_coords" format="tabular" label="${algorithm.value_label} coords">
+			<filter>make_coords=="yes"</filter>
+		</data>
+		<data name="out_delta" format="tabular" label="${algorithm.value_label} delta">
+			<filter>keep_delta=="yes"</filter>
+		</data>
+		<data name="out_png" format="png" label="${algorithm.value_label} mummerplot">
+			<filter>make_image=="yes"</filter>
+		</data>
+		<data name="out_log" format="tabular" label="Console log file">
+			<filter>keep_log=="yes"</filter>
+		</data>
+	</outputs>
+    <requirements>
+        <requirement type="package" version="4.6">gnuplot</requirement>
+        <requirement type="package" version="3.23">mummer</requirement>
+    </requirements>
+     <tests>
+    	<test>
+	      <param name="algorithm" value="nucmer" />
+	      <param name="input_ref" value="test.seq1.fasta"/>
+		  <param name="input_query" value="test.seq2.fasta"/>
+	      <param name="make_image" value="yes"/>
+		  <param name="keep_delta" value="no" />
+		  <param name="make_coords" value="no" />
+		  <param name="keep_log" value="yes" />	  
+		  
+	      <output name="out_log" file="test.MUMmerplot.result.Nucmer_galaxy.log" />
+	      <output name="out_png" file="test.MUMmerplot.result.Nucmer_galaxy.png" />        
+    	</test>
+	</tests>
+	<help>
+| 
+ 
+
+**Reference**
+-------------
+ 
+- **Nucmer Galaxy tool wrapper: Alex Bossers, CVI of Wageningen UR, The Netherlands.**
+
+- **Nucmer or Promer of MUMmer suite:** v3.22 http://mummer.sourceforge.net/manual/
+
+- **MUMmer tutorials:** http://mummer.sourceforge.net/examples/
+
+
+If you found these tools/wrappers useful in your research, please acknowledge our work. If you improve 
+or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)
+
+
+**Command line arguments**
+--------------------------
+
+--mum  Use anchor matches that are unique in both the reference and query 
+--mumreference  Use anchor matches that are unique in the reference but not necessarily unique in the query (default behavior) 
+--maxmatch  Use all anchor matches regardless of their uniqueness 
+--breaklen  Distance an alignment extension will attempt to extend poor scoring regions before giving up (default 200) 
+--mincluster  Minimum cluster length (default 65) 
+--delta  Toggle the creation of the delta file. Setting --nodelta prevents the alignment extension step and only outputs the match clusters (default --delta) 
+--depend  Print the dependency information and exit 
+--diagfactor  Maximum diagonal difference factor for clustering, i.e. diagonal difference / match separation (default 0.12) 
+--extend  Toggle the outward extension of alignments from their anchoring clusters. Setting --noextend will prevent alignment extensions but still align the DNA between clustered matches and create the .delta file (default --extend) 
+--forward  Align only the forward strands of each sequence 
+--maxgap  Maximum gap between two adjacent matches in a cluster (default 90) 
+--help  Print the help information and exit 
+--minmatch  Minimum length of an maximal exact match (default 20) 
+--optimize  Toggle alignment score optimization. Setting --nooptimize will prevent alignment score optimization and result in sometimes longer, but lower scoring alignments (default --optimize) 
+--reverse  Align only the reverse strand of the query sequence to the forward strand of the reference 
+--simplify  Simplify alignments by removing shadowed clusters. Turn this option off (--nosimplify) if aligning a sequence to itself to look for repeats (default --simplify) 
+--version  Print the version information and exit
+--coords  **Automatically ON in galaxy wrapper!** It generates the .coords file using the 'show-coords' program with the -r option. 
+--prefix  **Do NOT use in Galaxy wrapper!** Set the output file prefix (default out) 
+
+| 
+| 
+
+	</help>
+</tool>
+