--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mabcstats.xml	Tue Feb 21 06:37:00 2017 -0500
@@ -0,0 +1,85 @@
+<tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1">
+
+  <description>Run marker assisted backcrossing analysis on a dataset</description>
+
+  <command><![CDATA[
+  java
+  #if $advanced_options.show_advanced
+    -Xmx$advanced_options.memory
+  #end if
+  -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats
+  -map=$map
+  -genotypes=$genotypes
+  -qtls=$qtls
+  -parent1=$parent1
+  -parent2=$parent2
+  -model=$model
+  -coverage=$coverage
+  #if $advanced_options.show_advanced
+    $advanced_options.decimalEnglish
+  #end if
+  -output=$output
+  ]]></command>
+
+  <inputs>
+    <param format="fjmap" name="map" type="data" label="Flapjack map file"
+		help="Flapjack-formatted (tab-delimited text) input file of map data"/>
+	<param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
+		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
+	<param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
+		help="Flapjack-formatted (tab-delimited text) input file of QTL data"/>
+	<param name="parent1" type="integer" value="1" label="Index of recurrent parent"
+		help="The index of the recurrent parent in the genotype file"/>
+	<param name="parent2" type="integer" value="2" label="Index of donor parent"
+		help="The index of the donor parent in the genotype file"/>
+	<param name="model" type="select" label="Model"
+		help="The model to use for calculating statistics">
+	  <option selected="true" value="weighted">Weighted</option>
+	  <option value="unweighted">Unweighted</option>
+	</param>
+	<param name="coverage" type="float" value="10" label="Maximum coverage of a marker"
+		help="The maximum length of genome a marker can represent"/>
+	<conditional name="advanced_options">
+		<param name="show_advanced" type="boolean" label="Enable advanced options"
+			truevalue="show" falsevalue="">
+		</param>
+		<when value="show">
+			<param name="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
+            label="Force English-style decimal marks"
+            help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy's locale settings"/>
+			<param name="memory" type="select" label="Memory"
+				help="How much memory to use; larger files may require more memory">
+			  <option selected="true" value="64m">64MB</option>
+			  <option value="128m">128MB</option>
+			  <option value="256m">256MB</option>
+			</param>
+		</when>
+	</conditional>	
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+  
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+
+  <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
+allowing for rapid navigation and comparisons between lines, markers and chromosomes.
+
+This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
+See Flapjack's documentation_ for more details on the various Flapjack data formats.
+
+.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
+
+  ]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btq580</citation>
+  </citations>
+</tool>
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