# HG changeset patch
# User greg
# Date 1481730410 18000
# Node ID 755735c18b1ccb11faded6e9f0657734d98a8c8e
# Parent  d494b8f8989ca2dbbdb2c059352960a50afdb06f
Uploaded

diff -r d494b8f8989c -r 755735c18b1c multigps.xml
--- a/multigps.xml	Wed Dec 14 09:44:21 2016 -0500
+++ b/multigps.xml	Wed Dec 14 10:46:50 2016 -0500
@@ -90,6 +90,10 @@
                 ############################
                 ## Running MultiGPS
                 ############################
+                #if str($aoc.readdistributionfile) != 'None':
+                    --d "$aoc.readdistributionfile"
+                #end if
+                --r $aoc.maxtrainingrounds
                 #if str($aoc.nomodelupdate) == 'no':
                     --nomodelupdate
                 #end if
@@ -250,6 +254,8 @@
                 ## Running MultiGPS
                 ############################
                 -->
+                <param name="readdistributionfile" type="data" optional="True" format="tabular" label="Optional binding event read distribution file for initializing models" help="A default initial distribution appropriate for ChIP-seq data is used if this option is not specified." />
+                <param name="maxtrainingrounds" type="integer" value="3" min="0" label="Maximum number of training rounds for updating binding event read distributions" />
                 <param  name="nomodelupdate" type="select" label="Perform binding model updates?">
                     <option value="yes" selected="True">Yes</option>
                     <option value="no">No</option>