--- a/createproject.xml	Tue Aug 29 08:15:12 2017 -0400
+++ b/createproject.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -1,50 +1,107 @@
 <tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1">
+    <description>Create a Flapjack project file from the given input files.</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.CreateProject
+        -g $genotypes
+        -p $output
+        #if $map
+            -m $map
+        #end if
+        #if $name
+            -n $name
+        #end if
+        #if $qtls
+            -q $qtls
+        #end if
+        #if $traits
+            -t $traits
+        #end if
+        #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
+    ]]>
+    </command>
+    <inputs>
+        <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
+            help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
 
-<!--System.out.println("Usage: createproject <options>\n"
-				+ " where valid options are:\n"
-				+ "   -map=<map_file>                (optional input file)\n"
-				+ "   -genotypes=<genotypes_file>    (required input file)\n"
-				+ "   -traits=<traits_file>          (optional input file)\n"
-				+ "   -qtls=<qtl_file>               (optional input file)\n"
-				+ "   -decimalEnglish                (optional input parameter)\n"
-				+ "   -project=<project_file>        (required output file)\n");-->
+        <param format="fjmap" name="map" type="data" label="Flapjack map file"
+            help="Flapjack-formatted (tab-delimited text) input file of map data"
+            optional="true"/>
+
+        <param format="fjphenotype" name="traits" type="data" label="Flapjack phenotype file"
+            help="Flapjack-formatted (tab-delimited text) input file of phenotype data"
+            optional="true"/>
+
+        <param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
+            help="Flapjack-formatted (tab-delimited text) input file of QTL data"
+            optional="true"/>
+
+        <param format="text" name="name" type="text" label="Optional dataset name"
+            help="The name for the dataset within Flapjack"
+            optional="true"/>
 
-  <description>Run pedigree verification of F1s (known parents) analysis</description>
-  <command><![CDATA[
-  java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateProject 
-  -map=$map -genotypes=$genotypes
-##  -galaxyHTML=$html 
-  -project=$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"/>
+        <!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
+        <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 argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
-            label="Read input data using decimal English"
-            help="Build the index using a perfect hash rather than a dense hash.  This will require less memory
-			(especially during quantification), but will take longer to construct "/>
-	<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>
-  </inputs>
-  <outputs>
-  <!-- label="${tool.name} on ${on_string}: project.flapjack" -->
-    <data name="output" format="flapjack" />
-	<!--<data name="html" format="html" />-->
-  </outputs>
+                <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>
+        <!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
+    </inputs>
+
+    <outputs>
+        <data name="output" format="flapjack" />
+    </outputs>
   
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
 
-  <help><![CDATA[
+    <help><![CDATA[
 .. class:: infomark
 
 **What it does**
@@ -54,13 +111,13 @@
 
 This tool creates a Flapjack project file from the supplied tab-delimitted flapjack input files.
 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 
-
-
+More information on the CreateProject tool can be found here_
 
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
+.. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
+.. _here: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#createproject-exe-jhi-flapjack-io-createproject
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq580</citation>
+    </citations>
 </tool>
\ No newline at end of file