<tool id="mummer_maxmatch" name="MUMmer MaxMatch" version="0.9.alx" force_history_refresh="True">
  <description>: Maximal exact sequence matching</description>
  <command>
	<!-- update this path to the installed location -->
		$tool.cmd
		#if $tool.cmd=="mummer":
			$tool.cmd_extra
			$tool.mum_ref_in
			$tool.mum_q_in
		#end if
		#if $tool.cmd=="repeat-match":
			-n $tool.rm_n
			#if $tool.rm_E=="yes":
				-E
			#end if
			$tool.cmd_extra
			$tool.in_seq
		#end if
		#if $tool.cmd=="exact-tandems":
			$tool.in_seq
			$tool.et_minl
		#end if
		<!-- unfortunate somehow error state gets set also on succesfull jobs. Pipe io stderr to dev/null -->
		2&gt;&amp;-
		> $out_tool

  </command>
	<inputs>
	  <conditional name="tool">
		<param name="cmd" type="select" value="mummer" label="MUMmer maximal matching" help="Algorithms are run with default parameters (none). For specific args see help below" >
			<option value="mummer">mummer</option>
			<option value="repeat-match">repeat-match</option>
			<option value="exact-tandems">exact-tandems</option>
		</param>
		<when value="mummer">
			<param name="mum_ref_in" type="data" format="fasta" label="Reference FastA file" />
			<param name="mum_q_in" type="data" format="fasta" label="Query (multi) FastA sequence" />
			<param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="See specific cmd line options below for each tool" />
		</when>
		<when value="repeat-match">
			<param name="in_seq" type="data" format="fasta" label="FastA sequence file" />
			<param name="rm_n" type="text" size="5" value="20" label="Minimum exact match length [-n]" />
			<param name="rm_E" type="select" value="no" label="Use exhaustive (slow) search to find matches [-E]" >
				<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="-n and -E are configured above. More specific cmd line options in help below." />
		</when>
		<when value="exact-tandems">
			<param name="in_seq" type="data" format="fasta" label="FastA sequence file" />
			<param name="et_minl" type="text" size="5" value="20" label="Minimum length" />
		</when>
	  </conditional>
	</inputs>
	<outputs>
		<data name="out_tool" format="text" label="Max exact match output" />
	</outputs>
    <requirements>
<!--         <requirement type="set_environment" version="3.23">MUMMER_PATH</requirement> -->
        <requirement type="package" version="4.6.4">gnuplot</requirement>
        <requirement type="package" version="3.23">mummer</requirement>
    </requirements>
	<tests>
		<test>
		</test>
	</tests>
	<help>
|


**Reference**
=============
 
- **MUMmer MaxExactMatch Galaxy tool wrapper:** Alex Bossers, CVI of Wageningen UR, The Netherlands.

- **MUMmer suite v3.22:** http://mummer.sourceforge.net

- **MUMmer tutorials:** http://mummer.sourceforge.net/examples/

Please do not use any of the command line options that modify prefixes or file names. As obvious 
they are quite useless within galaxy and are likely to fail the routine!

If you found these tools/wrappers usefull in your research, please acknowledge our work. If you improve 
or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)



**MUMmer Maximal exact matching**
=================================

The heart of the MUMmer package is its suffix tree based maximal matching routines. These can be 
used for repeat detection within a single sequence as is done by *repeat-match* and *exact-tandems*, 
or can be used for the alignment of two or more sequences as is done by *mummer*.

Mummer
------

mummer is a suffix tree algorithm designed to find maximal exact matches of some minimum length 
between two input sequences. by default mummer will only find maximal matches that are unique in 
the entire set of reference sequences. The match lists produced by mummer can be used alone to 
generate alignment dot plots, or can be passed on to the clustering algorithms for the identification 
of longer non-exact regions of conservation. These match lists have great versatility because they 
contain huge amounts of information and can be passed forward to other interpretation programs for 
clustering, analysis, searching, etc.


Repeat-match
------------

repeat-match is a suffix tree algorithm designed to find maximal exact repeats within a single input 
sequence. It uses a similar algorithm to mummer, but altered slightly to find maximal exact matches 
within a single sequence.

Output formatting varies depending on the command line parameters and the output can be quite large. 
The standard output format that results from running repeat-match with default parameters is as follows:
::

 Long Exact Matches:
    Start1     Start2    Length
   4919485    4919506r       22

The three columns are the first position of the repeat, the second position of the repeat, and the 
length of the repeat respectively. Reverse complement repeat positions are denoted by an 'r' 
following the Start2 position, and are relative to the forward strand of the sequence.


Exact-tandems
-------------

exact-tandems is a wrapper script for the repeat-match program. It provides a list of exact tandem 
repeats within a single input sequence. As with repeat-match the sequence file should contain only 
one sequence in FastA format, however if multiple sequences exist the first one will be used. The 
sequence may contain any set of upper and lowercase characters, thus DNA and protein sequence are 
both allowed and matching is case insensitive. The minimum match length parameter should be a 
positive integer, this value will be passed to the repeat-match program via the -n option.

The output format of exact-tandems is as follows:
::

 Finding matches
 Tandem repeats
    Start   Extent  UnitLen     Copies
   416173      150       45        3.3

The four columns are the first position of the tandem, the extent of the repeat region, the length 
of each tandem repeat unit, and the number of repeat units respectively.



**Manuals and CMD line options (specific for each tool!):** 
===========================================================

**Mummer**

http://mummer.sourceforge.net/manual/#mummer

**Repeat-match**

http://mummer.sourceforge.net/manual/#repeat

**exact-tandems**

http://mummer.sourceforge.net/manual/#exact

| 
| 

	</help>
</tool>