diff admixture.xml @ 5:97c9c8daa3c3 draft

planemo upload

--- a/admixture.xml	Tue Apr 12 09:31:56 2016 -0400
+++ b/admixture.xml	Wed Apr 13 07:51:13 2016 -0400
@@ -3,7 +3,7 @@
 	<requirements>
 		<requirement type="package" version="1.23">admixture</requirement>
 	</requirements>
-	<command interpreter="bash">./admixture.sh $bed $fam $bim $outputs $logs $best_k_output $best_k_logfile $kmin $kmax
+	<command interpreter="bash">./admixture.sh $bed $fam $bim $outputs $logs $best_k_output $best_k_logfile $kmin $kmax $best_k_groups $threshold_group
     </command>
 	<inputs>
 		<param format="txt" name="bed" type="data" label="Allelic file in BED format" help="Allelic file in BED format"/>
@@ -11,9 +11,11 @@
 		<param format="txt" name="bim" type="data" label="Bim file" help="Bim file"/>
 		<param type="text" name="kmin" label="K min" value="2"/>
 		<param type="text" name="kmax" label="K max" value="5"/>
+		<param type="text" name="threshold_group" label="Minimum admixture proportion percentage for group assignation" value="50"/>
 	</inputs>
 	<outputs>
 		<data format="txt" name="best_k_output" label="Best K Output"/>
+		<data format="txt" name="best_k_groups" label="Best K Groups"/>
 		<data format="txt" name="best_k_logfile" label="Best K Logfile"/>
 		<data format="txt" name="outputs" label="All Outputs"/>
 		<data format="txt" name="logs" label="All Logs"/>
@@ -25,9 +27,10 @@
 			<param name="bim" value="input.bim" />
 			<param name="fam" value="input.fam" />
 			<param name="kmax" value="3" />
-
+			<param name="threshold_group" value="60" />
 			<output name="best_k_output" file="output" />
 			<output name="outputs" file="outputs.Q" />
+			<output name="best_k_groups" file="groups" />
 		</test>
 
 	</tests>
@@ -53,7 +56,6 @@
 
 -----
 
-
 ===========
  Overview:
 ===========
@@ -67,11 +69,7 @@
 
 .. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html
 	</help>
-
 <citations>
 <citation type="doi" >10.1101/gr.094052.109</citation>
 </citations>
-
-
-
 </tool>