--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ukseed_stage1.xml	Fri Apr 20 04:59:11 2018 -0400
@@ -0,0 +1,45 @@
+<tool id="ukseed_2_dartseq" name="UK SeeD (#2) Dartseq Analysis" version="0.0.1">
+    <description>run a dartseq analysis</description>
+    <requirements>
+        <!--
+		<requirement type="package" version="1.90b4">plink</requirement>
+		<requirement type="package" version="1.12.2">bioconductor-snprelate</requirement>
+		<requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>
+		<requirement type="package" version="0.8_14">r-amap</requirement>
+		<requirement type="package" version="1.2_16">r-rgdal</requirement>
+		<requirement type="package" version="1.0">r-dartr</requirement>
+		-->
+    </requirements>
+
+    <command><![CDATA[
+	    Rscript --vanilla $__tool_directory__/dartseq_seeduk_1b.R $input > $output
+    ]]></command>
+	
+    <inputs>
+        <param format="csv,txt" name="input" type="data" label="Input file"
+            help="Input file of genotype data"/>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+  
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+<help>
+In ``UK SeeD``, a BBSRC-Newton funded project, we have deployed an advanced computing hardware and software platform for the 
+analysis of large genomics datasets for wheat varieties. The platform integrates computing resources and bioinformatics expertise to 
+enable crop geneticists to implement sophisticated data analysis algorithms to improve the use of genetic resources for wheat and 
+other important crops. The computing platform is distributed across the partners’ sites with hardware deployed at CIMMYT (Mexico) and 
+the Earlham Institute (UK).  
+
+|JHI|
+
+.. |JHI| image:: https://ics.hutton.ac.uk/resources/ukseed/jhi.png
+</help>
+
+    <citations>
+    </citations>
+</tool>
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