--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hdf52fj.xml	Fri Feb 24 10:25:15 2017 -0500
@@ -0,0 +1,55 @@
+<tool id="flapjack_hdf52fj" name="HDF5 to Flapjack Tabbed Genotype Format" version="0.0.1">
+
+  <description>convert an HDF5 formatted genotype file into a Flapjack-formatted genotype file</description>
+  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.Hdf5ToFJTabbedConverter 
+	  -hdf5=$hdf5 
+	  -lines=$lines
+	  -markers=$markers
+	  -missing_filter=$missing_filter
+	  -heterozygous_filter=$heterozygous_filter
+	  -genotypes=$genotypes
+  </command>
+  <inputs>
+    <param format="h5" name="hdf5" type="data" label="Source file"
+		help="Flapjack's flavour of HDF5 for storing genotype data."/>
+	<param format="txt" name="lines" type="data" label="Source file"
+		help="A list of lines desired in the output. One line name per line on each line of the file."/>
+	<param format="txt" name="markers" type="data" label="Source file"
+		help="A list of markers desired in the output. One line name per marker on each line of the file."/>
+	<param name="missing_filter" type="boolean" label="Filter out missing markers"
+		truevalue="true" falsevalue="false">
+	</param>
+	<param name="heterozygous_filter" type="boolean" label="Filter out heterozygous markers"
+		truevalue="true" falsevalue="false">
+	</param>
+	<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="fjgenotype" name="genotypes" />
+  </outputs>
+
+  <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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