<tool id="mummer_tool" name="MUMmer" version="0.4.alx" force_history_refresh="True">
  <description>: Compare 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="binary">nucmer</requirement>
	  <requirement type="binary">promer</requirement>
	</requirements>
	<tests>
		<test>
		</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) 

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	</help>
</tool>