--- a/mabcstats.xml	Tue Aug 29 08:15:12 2017 -0400
+++ b/mabcstats.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -1,82 +1,120 @@
 <tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1">
-
-  <description>Run marker assisted backcrossing analysis on a dataset</description>
+	<description>Run marker assisted backcrossing (MABC) analysis on a dataset</description>
+	<command><![CDATA[
+		java
+		#if $adv_opts.show_advanced
+			-Xmx$adv_opts.memory
+		#end if
+		-cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats
+		-m $map
+		-g $genotypes
+		-q $qtls
+		-r $parent1
+		-d $parent2
+		-model $model
+		-c $coverage
+		-o $output
+		#if $adv_opts.show_advanced
+			$adv_opts.allChromosomes
+			$adv_opts.collapseHets
+			-M "$adv_opts.missingData"
+			-S "$adv_opts.hetSep"
+			$adv_opts.transposed
+			$adv_opts.decimalEnglish
+		#end if
+		#if $create_project
+			-p $project
+		#end if
+	]]></command>
 
-  <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
-  -m $map
-  -g $genotypes
-  -q $qtls
-  -r $parent1
-  -d $parent2
-  -model $model
-  -c $coverage
-  #if $advanced_options.show_advanced
-    $advanced_options.decimalEnglish
-  #end if
-  -o $output
-  #if $create_project  
-    -p $project
-  #end if	
-  ]]></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>
 
-  <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 name="coverage" type="float" value="10" label="Maximum coverage of a marker"
+			help="The maximum length of genome a marker can represent."/>
+
+		<conditional name="adv_opts">
+			<param name="show_advanced" type="boolean"
+				label="Enable advanced options"
+				truevalue="show" falsevalue="">
+			</param>
+			<when value="show">
+				<param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
+					label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
+					help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>
+
+				<param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
+					label="Don't distinguish between heterozygous alleles"
+					help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>
+
+				<param name="missingData" type="text" value="-"
+					label="Missing data string"
+					help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
+
+				<param name="hetSep" type="text" value="/"
+					label="Heterozygous allele separator string"
+					help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
+
+				<param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
+					label="Genotype data has been transposed"
+					help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>
+
+				<param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
+					label="Force English-style decimal marks"
+					help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server'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>
+
+		<param name="create_project" type="boolean" label="Also create Flapjack project file"
+			truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the MABC results.">
 		</param>
-		<when value="show">
-			<param name="decimalEnglish" type="boolean" truevalue="-D" 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>
-	
-	<param name="create_project" type="boolean" label="Also create Flapjack project file"
-		truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the MABC results.">
-	</param>
-  </inputs>
+	</inputs>
   
-  <outputs>
-    <data format="tabular" name="output" />
-	<data format="flapjack" name="project">
-		<filter>create_project</filter>
-	</data> 
-	
-  </outputs>
+	<outputs>
+		<data format="tabular" name="output" />
+		<data format="flapjack" name="project">
+			<filter>create_project</filter>
+		</data>
+	</outputs>
   
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
+	<stdio>
+		<exit_code range="1:" />
+	</stdio>
 
-  <help><![CDATA[
+	<help><![CDATA[
 .. class:: infomark
 
 **What it does**
@@ -84,13 +122,12 @@
 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.
+Flapjack documentation_
 
-.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
+.. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#mabcstats-exe-jhi-flapjack-io-generatemabcstats
+	]]></help>
 
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/btq580</citation>
+	</citations>
 </tool>
\ No newline at end of file