<tool id="mummer_utilities_tool" name="MUMmer utilities" version="0.9.alx" force_history_refresh="True">
  <description>: Show and filter on sequence delta file</description>
  <command>
  	<!-- update this path to the installed location -->
		$tool.cmd
		$cmd_extra
		$input_delta
		#if $tool.cmd=="show-aligns":
			$tool.aligns1
			$tool.aligns2
		#end if
		> $out_tool
  </command>
	<inputs>
	  <conditional name="tool">
		<param name="cmd" type="select" value="show-snps" label="MUMmer utility" help="Utilities are run with default parameters (none). For utility specific args see help below" >
			<option value="show-snps">show SNPs</option>
			<option value="show-tiling">show tiling</option>
			<option value="show-diff">show diff</option>
			<option value="show-coords">show coords</option>
			<option value="show-aligns">show aligns</option>
			<option value="delta-filter">delta filter</option>
		</param>
		<when value="show-aligns">
			<param name="aligns1" type="text" size="40" value="" label="IdR" help="the FastA header tag of the desired reference sequence" />
			<param name="aligns2" type="text" size="40" value="" label="IdQ" help="the FastA header tag of the desired query sequence" />
		</when>
		<when value="show-snps" />
		<when value="show-tiling" />
		<when value="show-coords" />
		<when value="show-diff" />
		<when value="delta-filter" />
 	  </conditional>
		<param name="input_delta" type="data" format="tabular" label="MUMmer delta file" />
		<param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="see specific cmd line options below for each tool" />
	</inputs>
	<outputs>
		<data name="out_tool" format="text" />
	</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_utilities Galaxy tool wrapper:** Alex Bossers, CVI of Wageningen UR, The Netherlands.

- **MUMmer utilities running on MUMmer delta file:** http://mummer.sourceforge.net/manual

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

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 Utilities**
====================

All tools are using the MUMmer generated DELTA file! Additional arguments are only required for show-aligns.

Show-coords
-----------

show-coords parses the delta alignment output of NUCmer and PROmer, and displays summary 
information such as position, percent identity and so on, of each alignment. It is the most 
commonly used tool for analyzing the delta files. *Usually the -r is used to sort lines by reference*


Show-tiling
-----------

show-tiling attempts to construct a tiling path out of the query contigs as mapped to the reference 
sequences. Given the delta alignment information of a few long reference sequences and many small 
query contigs, show-tiling will determine the best mapped location of each query contig. Note that 
each contig may only be tiled once, so repetitive regions may cause this program some difficulty. 
This program is useful for aiding in the scaffolding and closure of an unfinished set of contigs, 
if a suitable, high similarity reference genome is available. Or, if using PROmer, show-tiling will 
help in the identification of syntenic regions and their contig's mapping to the references.

This program is not suitable for "many vs. many" assembly comparisons, however a new tool based on 
the concepts of show-tiling should be available in the near future that will facilitate the mapping 
of assembly contigs.


Show-snps
---------

show-snps is a utility program for reporting polymorphisms contained in a delta encoded alignment 
file output by NUCmer or PROmer. It catalogs all of the single nucleotide polymorphisms (SNPs) and 
insertions/deletions within the delta file alignments. Polymorphisms are reported one per line, in 
a delimited fashion similar to show-coords. Pairing this program with the appropriate MUMmer tools 
can create an easy to use SNP pipeline for the rapid identification of putative SNPs between any 
two sequence sets, as demonstrated in the manual SNP detection section.


Show-diff
---------

Outputs a list of structural differences for each sequence in
the reference and query, sorted by position. For a reference
sequence R, and its matching query sequence Q, differences are
categorized as GAP (gap between two mutually consistent alignments),
DUP (inserted duplication), BRK (other inserted sequence), JMP
(rearrangement), INV (rearrangement with inversion), SEQ
(rearrangement with another sequence). The first five columns of
the output are seq ID, feature type, feature start, feature end,
and feature length. Additional columns are added depending on the
feature type. Negative feature lengths indicate overlapping adjacent
alignment blocks.
::

  IDR GAP gap-start gap-end gap-length-R gap-length-Q gap-diff
  IDR DUP dup-start dup-end dup-length
  IDR BRK gap-start gap-end gap-length
  IDR JMP gap-start gap-end gap-length
  IDR INV gap-start gap-end gap-length
  IDR SEQ gap-start gap-end gap-length prev-sequence next-sequence

Positions always reference the sequence with the given ID. The
sum of the fifth column (ignoring negative values) is the total
amount of inserted sequence. Summing the fifth column after removing
DUP features is total unique inserted sequence. Note that unaligned
sequence are not counted, and could represent additional "unique"
sequences. See documentation for tips on how to interpret these
alignment break features.


Show-aligns
-----------

show-aligns parses the delta encoded alignment output of NUCmer and PROmer, and displays 
the pair-wise alignments from the two sequences specified on the command line. It is handy 
for identifying the exact location of errors and looking for SNPs between two sequences.


Delta-filter
------------

delta-filter is a utility program for the manipulation of the delta encoded alignment files output 
by the NUCmer and PROmer pipelines. It takes a delta file as input and filters the information based 
on the various command line switches, outputting only the desired alignments to stdout. Options to filter by 
alignment length, identity, uniqueness and consistency are provided. Certain combinations of these 
options can greatly reduce the number of unwanted alignments in the delta file, thus making the output 
of programs such as show-coords more comprehendible.



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

**Show-coords**

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

**Show-tiling**

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

**Show-snps**

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

**Show-aligns**

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

**Delta-filter**

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


	</help>
</tool>