# HG changeset patch
# User jowong
# Date 1540560359 14400
# Node ID 69a2c1612c5fb6b1864f1b6aa9c0ef0ed7b99a62
# Parent  b98b3e9da1463c18bf86703dbdca30e32da5f98e
planemo upload

diff -r b98b3e9da146 -r 69a2c1612c5f prince.xml
--- a/prince.xml	Mon Oct 22 11:10:25 2018 -0400
+++ b/prince.xml	Fri Oct 26 09:25:59 2018 -0400
@@ -18,14 +18,19 @@
         </test>
     </tests>
     <help><![CDATA[
-        usage: prince [-h] [-bo BOOST_OUTPUT] [-to TARGET_OUTPUT] [-tmp TEMPLATES]
-              [-tf TARGET_FILE] [-bf BOOSTING_FILE] [-k K] [-cn COPYNUMBER]
+        usage: prince [-h] [-bo BOOST_OUTPUT] [-to TARGET_OUTPUT] [-tmp TEMPLATES] [-tf TARGET_FILE] [-bf BOOSTING_FILE] [-k K] [-cn COPYNUMBER]
 
 	Prince Options.
 
 	optional arguments:
-	  -h, --help            show this help message and exit
-          -bo                    time
+	  -h, --help            Show this help message and exit
+	  -bo, --boost_output   Output file for training data / training data used to predict copy numbers for queries
+          -to, --target_output  Output file for query copy number predictions
+          -tmp, --templates     VNTR templates. Default is for M.TB
+          -tf, --target_file    Target genome names in a text file
+          -bf, --boosting_file  Training genome file names in a text file
+          -k, --k               Kmer size used during read recruitment
+          -cn, --copynumber     Copy number used for training genome
 
     ]]></help>
     <citations>