# HG changeset patch
# User greg
# Date 1481653228 18000
# Node ID 0ea6413d66b26b8f593c2f2802db1fbbfecd748f
# Parent  fc857bf9678195d2f3a7ca5f62d2f03a77b23c4c
Uploaded

diff -r fc857bf96781 -r 0ea6413d66b2 multigps.xml
--- a/multigps.xml	Tue Dec 13 13:06:40 2016 -0500
+++ b/multigps.xml	Tue Dec 13 13:20:28 2016 -0500
@@ -7,30 +7,6 @@
     <command detect_errors="aggressive">
     <command>
         <![CDATA[
-            ## java -Xmx15G org.seqcode.projects.multigps.MultiGPS
-            ## --species "Saccharomyces cerevisiae;sacCer3"
-            ## --threads 2 
-            ## --expt $bampath/$name.bam
-            ## --ctrl $control
-            ## --format BAM
-            ## --scalewin 500
-            ## --q 0.05
-            ## --nodifftests 
-            ## --verbose
-            ## --mappability
-            ## --jointinmodel
-            ## --fixedmodelrange
-            ## --gaussmodelsmoothing
-            ## --gausssmoothparam 1
-            ## --minmodelupdateevents 50
-            ## --memepath $memePath
-            ## --mememinw 6
-            ## --mememaxw 18
-            ## --seq $genome
-            ## --exclude $exclude
-            ## --out $name > $name.out 2>&1
-            ##
-
             multigps
             ############################
             ## General options
@@ -63,13 +39,13 @@
                     #end if
                     --mappability $rloc.mappability
                 #end if
-                    #if str($rloc.nocache) == "yes":
-                        --nocache
-                    #end if
+                #if str($rloc.nocache) == "yes":
+                    --nocache
+                #end if
                 ############################
                 ## Scaling data
                 ############################
-                #if str($sdc.scale_data) == "yes":
+                #if str($sdc.scale_data) == 'yes':
                     #if str($sdc.scaling) == 'no':
                         --noscaling $sdc.scaling
                     #end if
@@ -78,7 +54,7 @@
                     #end if
                     #if str($sdc.regressionscale) == 'yes':
                         --regressionscale $sdc.regressionscale
-                    #endif
+                    #enf if
                     #if str($sdc.sessscale) == 'yes':
                         --sesscale $sdc.sesscale
                     #end if
@@ -93,22 +69,22 @@
                 ############################
                 ## Running MultiGPS
                 ############################
-                #if str($aoc.nomodelupdate) == "no":
+                #if str($aoc.nomodelupdate) == 'no':
                     --nomodelupdate
                 #end if
                 --minmodelupdateevents $aoc.minmodelupdateevents
-                #if str($bmsc.nomodelsmoothing) == "no":
+                #if str($bmsc.nomodelsmoothing) == 'no':
                     --nomodelsmoothing
                 #end if
                 --splinesmoothparam $aoc.splinesmoothparam
-                #if str($gmsc.gaussmodelsmoothing) == "yes":
+                #if str($gmsc.gaussmodelsmoothing) == 'yes':
                     --gaussmodelsmoothing
                     --gausssmoothparam $gmsc.gausssmoothparam
                 #end if
-                #if str($aoc.jointinmodel) == "yes":
+                #if str($aoc.jointinmodel) == 'yes':
                     --jointinmodel
                 #end if
-                #if str($aoc.fixedmodelrange) == "yes":
+                #if str($aoc.fixedmodelrange) == 'yes':
                     --fixedmodelrange
                 #end if
                 --prlogconf $aoc.prlogconf
@@ -116,14 +92,14 @@
                     --fixedalpha $aoc.fixedalpha
                 #end if
                 --alphascale $aoc.alphascale
-                #if str($aoc.mlconfignotshared) == "no":
+                #if str($aoc.mlconfignotshared) == 'no':
                     --mlconfignotshared
                 #end if
                 --exclude "$aoc.exclude"
                 ############################
                 ## MultiGPS priors
                 ############################
-                #if str($umc.use_motif) == "yes":
+                #if str($umc.use_motif) == 'yes':
                     #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]
@@ -140,13 +116,13 @@
                     #set mpc = $umc.multigps_priors_cond
                     --seq $seq_dir
                     --geninfo ${chromInfo}
-                    #if str($mpc.multigps_priors) == "yes":
+                    #if str($mpc.multigps_priors) == 'yes':
                         #set bmc = $mpc.both_motifs_cond
-                        #if str($mpc.noposprior) == "no":
+                        #if str($mpc.noposprior) == 'no':
                             --noposprior
                         #end if
                         --probshared $mpc.probshared
-                        #if str($bmc.nomotifs) == "yes":
+                        #if str($bmc.nomotifs) == 'yes':
                             --memenmotifs $bmc.memenmotifs
                             --mememinw $bmc.mememinw
                             --mememaxw $bmc.mememaxw
@@ -154,7 +130,7 @@
                             --nomotifs
                             #set mfoc = $bmc.nomotifprior_cond
                             --nomotifprior $mfoc.nomotifprior
-                            #if str($mfoc.nomotifprior) == "yes":
+                            #if str($mfoc.nomotifprior) == 'yes':
                                 --memenmotifs $mfoc.memenmotifs
                                 --mememinw $mfoc.mememinw
                                 --mememaxw $mfoc.mememaxw
@@ -165,10 +141,10 @@
                 ############################
                 ## Reporting binding events
                 ############################
-                #if str($rbec.report_binding_events) == "yes":
+                #if str($rbec.report_binding_events) == 'yes':
                     --q $rbec.minqvalue
                     --minfold $rbec.minfold
-                    #if str($rbec.nodifftests) == "no":
+                    #if str($rbec.nodifftests) == 'no':
                         --nodifftests
                     #end if
                     --edgerod $rbec.edgerod
@@ -177,7 +153,7 @@
             #end if
             --out "$output_html.files_path"
             > "$output_html"
-            ##if str($output_process_log) == "yes":
+            ##if str($output_process_log) == 'yes':
             ##    --output_process_path "$output_process"
             ###end if
         ]]>