# HG changeset patch
# User cropgeeks
# Date 1524216952 14400
# Node ID 5dab264e38c2e65f62bb0cca1bc50a844b193957
# Parent  8f9667afe1dce3f057bcfb6082481b77507a4ce1
Uploaded

diff -r 8f9667afe1dc -r 5dab264e38c2 ukseed.xml
--- a/ukseed.xml	Fri Apr 20 05:30:31 2018 -0400
+++ b/ukseed.xml	Fri Apr 20 05:35:52 2018 -0400
@@ -1,12 +1,12 @@
 <tool id="ukseed_dartseq" name="UK SeeD 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="1.12.2">bioconductor-snprelate</requirement>
+		<requirement type="package" version="1.90b4">plink</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>
+		<requirement type="package" version="1.8_0">r-labdsv</requirement>
+		<!--<requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>-->
     </requirements>
 
     <command><![CDATA[
@@ -18,7 +18,7 @@
     ]]></command>
 	
     <inputs>
-        <param format="csv" name="input" type="data" label="Input file"
+        <param format="csv,txt" name="input" type="data" label="Input file"
             help="Input file of genotype data"/>
     </inputs>
 
@@ -31,15 +31,15 @@
     </stdio>
 
 <help>
-In ``UK SeeD``, a BBSRC-Newton funded project, we have deployed an advanced computing hardware and software platform for the 
+In **UK-SeeD Data Analysis Infrastructure**, 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|
+|LOGOS|
 
-.. |JHI| image:: https://ics.hutton.ac.uk/resources/ukseed/jhi.png
+.. |LOGOS| image:: https://ics.hutton.ac.uk/resources/ukseed/logos.png
 </help>
 
     <citations>
diff -r 8f9667afe1dc -r 5dab264e38c2 ukseed_stage1.xml
--- a/ukseed_stage1.xml	Fri Apr 20 05:30:31 2018 -0400
+++ b/ukseed_stage1.xml	Fri Apr 20 05:35:52 2018 -0400
@@ -29,7 +29,7 @@
     </stdio>
 
 <help>
-In ``UK-SeeD Data Analysis Infrastructure``, a BBSRC-Newton funded project, we have deployed an advanced computing hardware and software platform for the 
+In **UK-SeeD Data Analysis Infrastructure**, 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 
diff -r 8f9667afe1dc -r 5dab264e38c2 ukseed_stage2.xml
--- a/ukseed_stage2.xml	Fri Apr 20 05:30:31 2018 -0400
+++ b/ukseed_stage2.xml	Fri Apr 20 05:35:52 2018 -0400
@@ -42,7 +42,7 @@
     </stdio>
 
 <help>
-In ``UK-SeeD Data Analysis Infrastructure``, a BBSRC-Newton funded project, we have deployed an advanced computing hardware and software platform for the 
+In **UK-SeeD Data Analysis Infrastructure**, 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