--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mummerplot.xml	Wed Dec 05 02:36:43 2018 -0500
@@ -0,0 +1,139 @@
+<tool id="mummer_mummerplot" name="Mummerplot" version="@MUMMER_VERSION@">
+    <description>Generate 2-D dotplot of aligned sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="5.2.3">gnuplot</requirement>
+    </expand>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        ln -s $reference_sequence reference.fa &&
+        ln -s $query_sequence query.fa &&
+        mummerplot
+            -b '$breaklen'
+            $color
+            $coverage
+            $filter
+            $fat
+            #if str($labels.IDs) == 'yes':
+                -IdR '$labels.ref_id'
+                -IdQ '$labels.query_id'
+            #end if
+            #if str($sequences.seq_input) == 'yes':
+                -R '$reference_sequence'
+                -Q '$query_sequence'
+                $sequences.layout
+            #end if
+            -s '$size'
+            -terminal png
+            -title '$title'
+            $snp
+            #if $range.custom == 'yes':
+                -x [$range.min_x:$range.max_x]
+                -y [$range.min_y:$range.max_y]
+            #end if
+            '$delta'
+        ]]>
+    </command>
+    <inputs>
+        <param name="delta" type="data" format="tabular" label="Match File" />
+        <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" />
+        <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" />
+        <expand macro="mumplot_input" >
+            <conditional name="sequences" >
+                <param name="seq_input" type="select" label="Plot an ordered set of reference/query sequences?" >
+                    <option value="no">NO</option>
+                    <option value="yes">YES</option>
+                </param>
+                <when value="yes">
+                    <param name="layout" type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
+                </when>
+                <when value="no" />
+            </conditional>
+        </expand>
+        <param name="extra_outs" type="select" label="Output files used to create the plot or just the plot?" >
+            <option value="plot">Just the plot</option>
+            <option value="all">All outputs</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="gnuplot" format="txt" from_work_dir="out.gp" label="${tool.name} on ${on_string}: gnuplot" >
+            <filter> extra_outs == 'all' </filter>
+        </data>
+        <data name="fplot" format="txt" from_work_dir="out.fplot" label="${tool.name} on ${on_string}: fplot" >
+            <filter> extra_outs == 'all' </filter>
+        </data>
+        <data name="rplot" format="txt" from_work_dir="out.rplot" label="${tool.name} on ${on_string}: rplot" >
+            <filter> extra_outs == 'all' </filter>
+        </data>
+        <data name="hplot" format="txt" from_work_dir="out.hplot" label="${tool.name} on ${on_string}: hplot" >
+            <filter> extra_outs == 'all' </filter>
+        </data>
+        <data name="output_png" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="delta" ftype="txt" value="nucmer.txt" />
+            <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
+            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
+            <param name="seq_input" value="no" />
+            <param name="extra_outs" value="all" />
+            <output name="gnuplot" ftype="txt" compare="diff" value="gnuplot.txt" />
+            <output name="fplot" ftype="txt" compare="diff" value="fplot.txt" />
+            <output name="rplot" ftype="txt" compare="diff" value="rplot.txt" />
+            <output name="hplot" ftype="txt" compare="diff" value="hplot.txt" />
+            <output name="output_png" ftype="png" compare="sim_size" value="plot.png" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Mummerplot is a perl script that generates gnuplot scripts and data collections for plotting with the gnuplot utility. It can generate 2-d dotplots and 1-d coverage plots for the output of mummer or nucmer. It can also color dotplots with an identity color gradient.
+
+**Outputs:**
+    * gnuplot: The gnuplot script
+    * fplot, rplot, hplot: The forward, reverse, and highlighted match information for plotting with gnuplot.
+    * plot: The plotted image file
+
+**Options:**::
+
+
+    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest 
+                   sequence end
+
+    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default 
+                   color by match dir) If the plot is very sparse, edit the .gp script to plot with 
+                   'linespoints' instead of 'lines'
+
+    -c             Generate a reference coverage plot (default for .tiling)
+
+    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on 
+                   either sequence, i.e. a one-to-one mapping of reference and query subsequences
+
+    --fat          Layout sequences using fattest alignment only
+
+    -IdR           Plot a particular reference sequence ID on the X-axis
+
+    -IdQ           Plot a particular query sequence ID on the Y-axis
+
+    -s             Set the output size to small, medium or large (--small) (--medium) (--large) (default 'small')
+
+    --SNP          Highlight SNP locations in each alignment
+
+    -title         Specify the gnuplot plot title (default none)
+
+    -x             Set the xrange for the plot '[min:max]'
+
+    -y             Set the yrange for the plot '[min:max]'
+
+    -R             Plot an ordered set of reference sequences from Rfile
+
+    -Q             Plot an ordered set of query sequences from Qfile
+
+    --layout       Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options
+
+    ]]></help>
+    <expand macro="citation" />
+</tool>
+
+
+