--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Dec 05 02:38:25 2018 -0500
@@ -0,0 +1,69 @@
+<macros>
+    <xml name="citation">
+        <citations>
+            <citation type="bibtex">
+                @misc{githubmummer,
+                author = {Art Delcher, Stefan Kurtz, Adam Phillippy, Steven Salzberg},
+                year = {2012},
+                title = {mummer4},
+                publisher = {GitHub},
+                journal = {GitHub repository},
+                url = {https://github.com/mummer4/mummer},
+            }</citation>
+        </citations>
+    </xml>
+    <token name="@MUMMER_VERSION@">4.0.0beta2</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@MUMMER_VERSION@">mummer4</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="mumplot_input" >
+        <yield />
+        <param name="breaklen" type="integer" argument="-b" value="20" label="Break Length"
+            help="Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)" />
+        <param name="color" type="select" label="Color" help="Color plot lines with a percent similarity gradient or turn off all plot color." >
+            <option value="">Color</option>
+            <option value="-color">No color (-color)</option>
+        </param>
+        <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the defualt dotplot." >
+            <option value="">Dotplot</option>
+            <option value="-c">Coverage Plot (-c)</option>
+        </param>
+        <param name="filter" type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
+            help="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. (--filter)" />
+        <param name="fat" type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
+        <conditional name="labels" >
+            <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." >
+                <option value="no">NO</option>
+                <option value="yes">YES</option>
+            </param>
+            <when value="yes" >
+                <param name="ref_id" type="text" value="ref_id" label="Reference sequence ID" help="(-IdR)" />
+                <param name="query_id" type="text" value="query_id" label="Query sequence ID" help="(-IdQ)" />
+            </when>
+            <when value="no" />
+        </conditional>
+        <param name="size" type="select" label="Plot Size" help="Set the output size to small, medium or large. (-s)" >
+            <option value="small">Small</option>
+            <option value="medium">Medium</option>
+            <option value="large">Large</option>
+        </param>
+        <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" />
+        <param name="title" type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
+        <conditional name="range" >
+            <param name="custom" type="select" label="Choose custom X and Y axis ranges?" >
+                <option value="no">NO</option>
+                <option value="yes">YES</option>
+            </param>
+            <when value="yes" >
+                <param name="min_x" type="integer" argument="-x" value="0" label="Minimum X-axis range" help="(-x)" />
+                <param name="max_x" type="integer" argument="-x" value="100" label="Maximum X-axis range" help="(-x)" />
+                <param name="min_y" type="integer" argument="-y" value="0" label="Minimum Y-axis range" help="(-y)" />
+                <param name="max_y" type="integer" argument="-y" value="100" label="Maximum Y-axis range" help="(-y)" />
+            </when>
+            <when value="no" />
+        </conditional>
+    </xml>
+</macros>