--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MUMmer/mummer_utilities_tool.xml	Tue Mar 31 14:19:49 2015 +0200
@@ -0,0 +1,184 @@
+<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>
+