--- a/multigps.xml	Tue Feb 21 09:43:52 2017 -0500
+++ b/multigps.xml	Tue Feb 21 10:34:57 2017 -0500
@@ -11,9 +11,7 @@
             #set output_dir = $output_html.files_path
             mkdir -p $output_dir &&
             multigps
-            ############################
             ## General options
-            ############################
             ## Append .txt extensions to events hrefs
             ## in output dataset so files will render
             ## in the browser.
@@ -28,9 +26,7 @@
             #end if
             --threads=\${GALAXY_SLOTS:-4}
             --geninfo '$chromInfo'
-            ############################
             ## Advanced options
-            ############################
             #set aoc = $advanced_options_cond
             #if str($aoc.advanced_options) == 'display':
                 #set bmsc = $aoc.binding_model_smoothing_cond
@@ -48,9 +44,7 @@
                     #end if
                     --seq '$seq'
                 #end if
-                ############################
                 ## Limits on how many reads
-                ############################
                 #if str($rloc.reads_limits) == 'yes':
                     --fixedpb $rloc.fixedpb
                     --poissongausspb $rloc.poissongausspb
@@ -62,9 +56,7 @@
                         --nocache
                     #end if
                 #end if
-                ############################
                 ## Scaling data
-                ############################
                 #if str($sdc.scale_data) == 'yes':
                     #if str($sdc.scaling) == 'no':
                         --noscaling $sdc.scaling
@@ -86,9 +78,7 @@
                         --plotscaling $sdc.plotscaling
                     #end if
                 #end if
-                ############################
                 ## Running MultiGPS
-                ############################
                 #if str($aoc.readdistributionfile) != 'None':
                     --d '$aoc.readdistributionfile'
                 #end if
@@ -123,9 +113,7 @@
                 #if str($aoc.exclude) != 'None':
                     --exclude '$aoc.exclude'
                 #end if
-                ############################
                 ## MultiGPS priors
-                ############################
                 #if str($umc.use_motif) == 'yes':
                     #set mpc = $umc.multigps_priors_cond
                     #if str($mpc.multigps_priors) == 'yes':
@@ -150,9 +138,7 @@
                         #end if
                     #end if
                 #end if
-                ############################
                 ## Reporting binding events
-                ############################
                 #if str($rbec.report_binding_events) == 'yes':
                     --q $rbec.minqvalue
                     --minfold $rbec.minfold
@@ -164,9 +150,9 @@
                 #end if
             #end if
             --out '$output_html.files_path'
-            && mv $output_dir/*.html $output_html
-            && mv $output_dir/*.table.txt $all_events_table
-            && mv $output_dir/*.counts $replicates_counts
+            && mv $output_dir/*.html $output_html || true
+            && mv $output_dir/*.table.txt $all_events_table || true
+            && mv $output_dir/*.counts $replicates_counts || true
         ]]>
     </command>
     <inputs>
@@ -174,22 +160,14 @@
             <validator type="unspecified_build" />
         </param>
         <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" />
-        <!--
-        ############################
-        ## Advanced options
-        ############################
-        -->
+        <!-- Advanced options -->
         <conditional name="advanced_options_cond">
             <param name="advanced_options" type="select" label="Advanced options">
                 <option value="hide" selected="true">Hide</option>
                 <option value="display">Display</option>
             </param>
             <when value="display">
-                <!--
-                ############################
-                ## Limits on how many reads
-                ############################
-                -->
+                <!-- Limits on how many reads -->
                 <conditional name="reads_limits_options_cond">
                     <param name="reads_limits" type="select" label="Set limits on how many reads can have their 5′ end at the same position in each replicate?" help="Default behavior is to estimate a global per-base limit from a Poisson distribution parameterized by the number of reads divided by the number of mappable bases in the genome. The per-base limit is set as the count corresponding to the 10^-7 probability level from the Poisson.">
                         <option value="no" selected="True">No</option>
@@ -210,11 +188,7 @@
                         </param>
                     </when>
                 </conditional>
-                <!--
-                ############################
-                ## Scaling data
-                ############################
-                -->
+                <!-- Scaling data -->
                 <conditional name="scale_data_cond">
                     <param  name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using regression on the set of signal/control ratios in 10Kbp windows.">
                         <option value="no" selected="True">No</option>
@@ -246,11 +220,7 @@
                     </when>
                     <when value="no" />
                 </conditional>
-                <!--
-                ############################
-                ## Running MultiGPS
-                ############################
-                -->
+                <!-- 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?">
@@ -294,22 +264,14 @@
                     <option value="no">No</option>
                 </param>
                 <param name="exclude" type="data" optional="True" format="txt" label="Optional file containing a set of regions to ignore during MultiGPS training" help="Ideally exclude the mitochondrial genome and other blacklisted regions that contain artifactual accumulations of reads in both ChIP-seq and control experiments." />
-                <!--
-                ############################
-                ## MultiGPS priors
-                ############################
-                -->
+                <!-- MultiGPS priors -->
                 <conditional name="use_motif_cond">
                     <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?">
                         <option value="no" selected="True">No</option>
                         <option value="yes">Yes</option>
                     </param>
                     <when value="yes">
-                        <!--
-                        ############################
-                        ## Specifying the genome
-                        ############################
-                        -->
+                        <!-- Specifying the genome -->
                         <conditional name="reference_genome_cond">
                             <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
                                 <option value="cached">locally cached</option>
@@ -332,11 +294,7 @@
                                 </param>
                             </when>
                         </conditional>
-                        <!--
-                        ############################
-                        ## MultiGPS priors options
-                        ############################
-                        -->
+                        <!-- MultiGPS priors options -->
                         <conditional name="multigps_priors_cond">
                             <param name="multigps_priors" type="select" label="Specify MultiGPS priors options?">
                                 <option value="no" selected="True">No</option>
@@ -375,11 +333,7 @@
                     </when>
                     <when value="no" />
                 </conditional>
-                <!--
-                ############################
-                ## Reporting binding events
-                ############################
-                -->
+                <!-- Reporting binding events -->
                 <conditional name="report_binding_events_cond">
                     <param name="report_binding_events" type="select" label="Report binding events?">
                         <option value="no" selected="True">No</option>
@@ -492,5 +446,7 @@
  - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment.
 
     </help>
-    <expand macro="citations" />
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1003501</citation>
+    </citations>
 </tool>