# HG changeset patch
# User greg
# Date 1481720048 18000
# Node ID 32a59270224bfe053497a79e159e8b0be07b4001
# Parent  d5c1ab05259bb5e33dbe2d643adf0fd978da189c
Uploaded

diff -r d5c1ab05259b -r 32a59270224b multigps.xml
--- a/multigps.xml	Wed Dec 14 07:45:02 2016 -0500
+++ b/multigps.xml	Wed Dec 14 07:54:08 2016 -0500
@@ -30,10 +30,6 @@
             #set rloc = $aoc.reads_limits_options_cond
             #set sdc = $aoc.scale_data_cond
             #set umc = $aoc.use_motif_cond
-            #set mpc = $umc.multigps_priors_cond
-            #set bmc = $mpc.both_motifs_cond
-            #set mfoc = $bmc.nomotifprior_cond
-            #set rgc = $umc.reference_genome_cond
             #if str($aoc.advanced_options) == 'display':
                 ############################
                 ## Limits on how many reads
@@ -107,6 +103,8 @@
                 ## MultiGPS priors
                 ############################
                 #if str($umc.use_motif) == 'yes':
+                    #set mpc = $umc.multigps_priors_cond
+                    #set rgc = $umc.reference_genome_cond
                     #if str($rgc.reference_genome_source) == "cached":
                         #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0]
                     #else:
@@ -122,6 +120,7 @@
                     --seq $seq_dir
                     --geninfo ${chromInfo}
                     #if str($mpc.multigps_priors) == 'yes':
+                        #set bmc = $mpc.both_motifs_cond
                         #if str($mpc.noposprior) == 'no':
                             --noposprior
                         #end if
@@ -131,6 +130,7 @@
                             --mememinw $bmc.mememinw
                             --mememaxw $bmc.mememaxw
                         #else:
+                            #set mfoc = $bmc.nomotifprior_cond
                             --nomotifs
                             --nomotifprior $mfoc.nomotifprior
                             #if str($mfoc.nomotifprior) == 'yes':