--- a/multigps.xml	Wed Dec 14 11:31:49 2016 -0500
+++ b/multigps.xml	Wed Feb 08 12:57:32 2017 -0500
@@ -1,27 +1,29 @@
-<tool id="multigps" name="MultiGPS" version="0.72.0">
+<tool id="multigps" name="MultiGPS" version="0.73">
     <description>analyzes collections of multi-condition ChIP-seq data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.72">multigps</requirement>
+        <requirement type="package" version="0.73">multigps</requirement>
     </requirements>
     <command detect_errors="aggressive">
         <![CDATA[
+            #set output_dir = $output_html.files_path
+            mkdir -p $output_dir &&
             multigps
             ############################
             ## General options
             ############################
-            --expt "$expt"
-            --format "$expt.ext"
-            #if $ctrl is not None:
-                --ctrl "$ctrl"
+            --expt '$expt'
+            --format $expt.ext
+            #if str($ctrl) != 'None':
+                --ctrl '$ctrl'
             #end if
             #if str($verbose) == 'yes':
                 --verbose
             #end if
-            --threads="\${GALAXY_SLOTS:-4}"
-            --geninfo "$chromInfo"
+            --threads=\${GALAXY_SLOTS:-4}
+            --geninfo '$chromInfo'
             ############################
             ## Advanced options
             ############################
@@ -33,17 +35,17 @@
                 #set rloc = $aoc.reads_limits_options_cond
                 #set sdc = $aoc.scale_data_cond
                 #set umc = $aoc.use_motif_cond
-                #if str($umc.use_motif) == "yes":
+                #if str($umc.use_motif) == 'yes':
                     #set rgc = $umc.reference_genome_cond
-                    #if str($rgc.reference_genome_source) == "cached":
+                    #if str($rgc.reference_genome_source) == 'cached':
                         #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0]
                     #else:
                         ## MultiGPS requires a directory containing reference files, so symlink the history dataset.
                         #import os
                         #import tempfile
-                        #set seq_dir = tempfile.mkdtemp(prefix="tmp-multigps-seq-dir")
+                        #set seq_dir = tempfile.mkdtemp(prefix='tmp-multigps-seq-dir')
                         #set seq_file = str($rgc.reference_genome)
-                        #set tmp_filename = "%s.fa" % str($rgc.reference_genome.dbkey)
+                        #set tmp_filename = '%s.fa' % str($rgc.reference_genome.dbkey)
                         #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename)
                         ln -f -s $tmp_seq_file $seq_file &&
                     #end if
@@ -91,7 +93,7 @@
                 ## Running MultiGPS
                 ############################
                 #if str($aoc.readdistributionfile) != 'None':
-                    --d "$aoc.readdistributionfile"
+                    --d '$aoc.readdistributionfile'
                 #end if
                 --r $aoc.maxtrainingrounds
                 #if str($aoc.nomodelupdate) == 'no':
@@ -122,7 +124,7 @@
                     --mlconfignotshared
                 #end if
                 #if str($aoc.exclude) != 'None':
-                    --exclude "$aoc.exclude"
+                    --exclude '$aoc.exclude'
                 #end if
                 ############################
                 ## MultiGPS priors
@@ -164,15 +166,17 @@
                     --diffp $rbec.diffp
                 #end if
             #end if
-            --out "$output_html.files_path"
-            > "$output_html"
+            --out '$output_html.files_path'
+            && mv $output_dir/*.html $output_html
+            && mv $output_dir/*.table $all_events_table
+            && mv $output_dir/*.counts $replicates_counts
         ]]>
     </command>
     <inputs>
         <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
             <validator type="unspecified_build" />
         </param>
-        <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing file containing reads from a control experiment" help="Must be same forat as the input above" />
+        <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" />
         <param name="verbose" type="select" label="Generate intermediate files and extra output?" help="Verbose flag">
             <option value="no" selected="True">No</option>
             <option value="yes">Yes</option>
@@ -411,23 +415,27 @@
         -->
     </inputs>
     <outputs>
-        <data name="output_html" format="html"/>
+        <data name="output_html" format="html" label="Results (HTML) on ${on_string}"/>
+        <data name="all_events_table" format="tabular" label="All events table on ${on_string}"/>
+        <data name="replicates_counts" format="tabular" label="Replicates counts on ${on_string}"/>
     </outputs>
     <tests>
         <test>
-            <param name="expt" value="sacCer3_1.scidx" ftype="scidx" dbkey="sacCer3"/>
-            <param name="binding_model_smoothing" value="no"/>
-            <param name="gaussmodelsmoothing" value="yes"/>
-            <param name="gausssmoothparam" value="3"/>
-            <param name="use_motif" value="yes"/>
-            <param name="reference_genome_source" value="history"/>
-            <param name="reference_genome" value="phiX.fasta" dbkey="phiX"/>
-            <param name="memenmotifs" value="3"/>
-            <param name="mememinw" value="6"/>
-            <param name="mememaxw" value="16"/>
-            <param name="output_process_log" value="yes"/>
-            <output name="output_process" file="output_process1.txt" ftype="txt" lines_diff="12"/>
-            <output name="output_html" file="output_html1.html" ftype="html" lines_diff="12"/>
+            <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="sacCer3" />
+            <param name="verbose" value="no" />
+            <param name="advanced_options_cond" value="hide" />
+            <output name="output_html" file="hg19_output_html1.html" ftype="html" lines_diff="12"/>
+            <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
+            <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="sacCer3" />
+            <param name="ctrl" value="cntrl_hg19.scidx" ftype="bam" dbkey="sacCer3" />
+            <param name="verbose" value="no" />
+            <param name="advanced_options_cond" value="display" />
+            <output name="output_html" file="hg19_output_html2.html" ftype="html" lines_diff="12"/>
+            <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
+            <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>
         </test>
     </tests>
     <help>
@@ -446,7 +454,7 @@
 
 * **Loading data:**
 
- - **Optional file containing file containing reads from a control experiment** - must be same format as input experiment
+ - **Optional file containing reads from a control experiment** - must be same format as input experiment
  - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model).
  - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be.
  - **Use non-unique reads** - Use non-unique reads.