--- a/fj2hdf5.xml	Tue Aug 29 08:15:12 2017 -0400
+++ b/fj2hdf5.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -1,21 +1,44 @@
 <tool id="flapjack_fj2hdf5" name="Flapjack to HDF5" version="0.0.1">
-  <description>convert a Flapjack-formatted genotype file into HDF5</description>
-  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter -genotypes=$input_genotypes -hdf5=$output_hdf5</command>
-  <inputs>
-    <param format="csv,tabular,txt" name="input_genotypes" type="data" label="Source file"
-		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
-	<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>
-    <data format="h5" name="output_hdf5" />
-  </outputs>
+    <description>Convert a Flapjack-formatted genotype file into HDF5</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.FJTabbedToHdf5Converter
+        -g $genotypes
+        -h $output
+    ]]></command>
+    <inputs>
+        <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
+            help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
 
-  <help><![CDATA[
+        <conditional name="adv_opts">
+            <param name="show_advanced" type="boolean"
+                label="Enable advanced options"
+                truevalue="show" falsevalue="">
+            </param>
+            <when value="show">
+                <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="h5" name="output" />
+    </outputs>
+
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <help><![CDATA[
 .. class:: infomark
 
 **What it does**
@@ -26,12 +49,10 @@
 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 
-
-
+.. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
+    ]]></help>
 
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq580</citation>
+    </citations>
 </tool>
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