--- a/multigps.xml	Mon Mar 06 09:17:58 2017 -0500
+++ b/multigps.xml	Wed Sep 05 08:54:21 2018 -0400
@@ -1,10 +1,10 @@
-<tool id="multigps" name="MultiGPS" version="0.73.0">
+<tool id="multigps" name="MultiGPS" version="0.74.0">
     <description>analyzes collections of multi-condition ChIP-seq data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.73">multigps</requirement>
+        <requirement type="package" version="0.74">multigps</requirement>
     </requirements>
     <command detect_errors="aggressive">
         <![CDATA[
@@ -12,19 +12,14 @@
             mkdir -p $output_dir &&
             multigps
             ## General options
+            --design '$build_design_file'
             ## Append .txt extensions to events hrefs
             ## in output dataset so files will render
             ## in the browser.
             --eventsaretxt
-            ## Do not run the parallel version of meme
-            ## since it is not yet available in conda.
+            ## Do not run the parallel version of meme.
             --meme1proc
-            --expt '$expt'
-            --format $expt.ext
-            #if str($ctrl) != 'None':
-                --ctrl '$ctrl'
-            #end if
-            --threads=\${GALAXY_SLOTS:-4}
+            --threads \${GALAXY_SLOTS:-4}
             --geninfo '$chromInfo'
             ## Advanced options
             #set aoc = $advanced_options_cond
@@ -37,12 +32,12 @@
                 #set umc = $aoc.use_motif_cond
                 #if str($umc.use_motif) == 'yes':
                     #set rgc = $umc.reference_genome_cond
+                    --seq
                     #if str($rgc.reference_genome_source) == 'cached':
-                        #set seq = $rgc.reference_genome.fields.path
+                        '${rgc.reference_genome.fields.path}'
                     #else:
-                        #set seq = $rgc.reference_genome
+                        '${rgc.reference_genome}'
                     #end if
-                    --seq '$seq'
                 #end if
                 ## Limits on how many reads
                 #if str($rloc.reads_limits) == 'yes':
@@ -80,9 +75,9 @@
                 #end if
                 ## Running MultiGPS
                 #if str($aoc.readdistributionfile) != 'None':
-                    --d '$aoc.readdistributionfile'
+                    --readdistributionfile '$aoc.readdistributionfile'
                 #end if
-                --r $aoc.maxtrainingrounds
+                --maxtrainingrounds $aoc.maxtrainingrounds
                 #if str($aoc.nomodelupdate) == 'no':
                     --nomodelupdate
                 #end if
@@ -127,20 +122,20 @@
                             --mememinw $bmc.mememinw
                             --mememaxw $bmc.mememaxw
                         #else:
-                            #set mfoc = $bmc.nomotifprior_cond
+                            #set nmpc = $bmc.nomotifprior_cond
                             --nomotifs
-                            --nomotifprior $mfoc.nomotifprior
-                            #if str($mfoc.nomotifprior) == 'yes':
-                                --memenmotifs $mfoc.memenmotifs
-                                --mememinw $mfoc.mememinw
-                                --mememaxw $mfoc.mememaxw
+                            #if str($nmpc.nomotifprior) == 'yes':
+                                --nomotifprior
+                                --memenmotifs $nmpc.memenmotifs
+                                --mememinw $nmpc.mememinw
+                                --mememaxw $nmpc.mememaxw
                             #end if
                         #end if
                     #end if
                 #end if
                 ## Reporting binding events
                 #if str($rbec.report_binding_events) == 'yes':
-                    --q $rbec.minqvalue
+                    --minqvalue $rbec.minqvalue
                     --minfold $rbec.minfold
                     #if str($rbec.nodifftests) == 'no':
                         --nodifftests
@@ -149,19 +144,78 @@
                     --diffp $rbec.diffp
                 #end if
             #end if
-            >/dev/null
+            2>&1
             --out '$output_html.files_path'
-            && cp $output_dir/*.events.txt '$experiment_events' || true
-            && mv $output_dir/*.html '$output_html' || true
-            && mv $output_dir/*.table.txt '$all_events_table' || true
-            && mv $output_dir/*.counts '$replicates_counts' || true
+            #if str($save_design_file) == 'yes':
+                && cp '$build_design_file' '$output_design_file'
+            #end if
+            && mv $output_dir/*.counts '$replicates_counts'
+            && mv $output_dir/*.bed '$output_bed'
+            && mv $output_dir/*.html '$output_html'
+            && mv $output_dir/*.table.txt '$all_events_table'
         ]]>
     </command>
+    <configfiles>
+        <configfile name="build_design_file"><![CDATA[#for $condition_items in $condition_repeat:
+    #for $signal_items in $condition_items.signal_repeat:
+        #if str($signal_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
+            #set $frc = $signal_items.fixedreadcount_cond.fixedreadcount
+        #else:
+            #set $frc = ''
+        #end if
+${signal_items.signal}	Signal	${signal_items.signal.ext.upper()}	${condition_items.condition_name}	${signal_items.replicate_name}	${condition_items.experiment_type}	${frc}
+    #end for
+    #for $control_items in $condition_items.control_repeat:
+        #if str($control_items.specify_replicate_name_cond.specify_replicate_name) == 'yes':
+            #set $rn = $control_items.specify_replicate_name_cond.replicate_name
+        #else:
+            #set $rn = ''
+        #end if
+        #if str($control_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
+            #set $frc = $control_items.fixedreadcount_cond.fixedreadcount
+        #else:
+            #set $frc = ''
+        #end if
+${control_items.control}	Control	${control_items.control.ext.upper()}	${condition_items.condition_name}	${rn}	${condition_items.experiment_type}	${frc}
+    #end for
+#end for ]]></configfile>
+    </configfiles>
     <inputs>
-        <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
-            <validator type="unspecified_build" />
+        <repeat name="condition_repeat" title="Condition" min="1">
+            <param name="condition_name" type="text" value="cond" label="Condition name">
+                <validator type="empty_field" />
+            </param>
+            <expand macro="param_experiment_type" />
+            <repeat name="signal_repeat" title="Signal" min="1">
+                <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx">
+                    <validator type="unspecified_build" />
+                </param>
+                <param name="replicate_name" type="text" value="1" label="Replicate name">
+                    <validator type="empty_field" />
+                </param>
+                <expand macro="cond_fixedreadcount" />
+            </repeat>
+            <repeat name="control_repeat" title="Control" min="0">
+                <param name="control" type="data" format="bam,bed,scidx" label="Select control" help="Optional, supported formats are bam, bed and scidx">
+                    <validator type="unspecified_build" />
+                </param>
+                <conditional name="specify_replicate_name_cond">
+                    <param  name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control.  If used, the control will only be used for the corresponding named signal replicate">
+                        <option value="no" selected="True">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="yes">
+                        <param name="replicate_name" type="text" optional="true" label="Replicate name"/>
+                    </when>
+                    <when value="no" />
+                </conditional>
+                <expand macro="cond_fixedreadcount" />
+            </repeat>
+        </repeat>
+        <param name="save_design_file" type="select" display="radio" label="Output design file?">
+            <option value="no" selected="true">No</option>
+            <option value="yes">Yes</option>
         </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 -->
         <conditional name="advanced_options_cond">
             <param name="advanced_options" type="select" label="Advanced options">
@@ -192,7 +246,7 @@
                 </conditional>
                 <!-- 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.">
+                    <param  name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using the Normalization of ChIP-seq (NCIS) method.[2]">
                         <option value="no" selected="True">No</option>
                         <option value="yes">Yes</option>
                     </param>
@@ -282,7 +336,7 @@
                             <when value="cached">
                                 <param name="reference_genome" type="select" label="Using reference genome">
                                     <options from_data_table="all_fasta">
-                                        <filter type="data_meta" key="dbkey" ref="expt" column="1"/>
+                                        <!-- <filter type="data_meta" key="dbkey" ref="expt" column="1"/> does not yet work in a repeat...-->
                                     </options>
                                     <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                                 </param>
@@ -290,7 +344,7 @@
                             <when value="history">
                                 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
                                     <options>
-                                        <filter type="data_meta" key="dbkey" ref="expt"/>
+                                        <!-- <filter type="data_meta" key="dbkey" ref="expt"/> does not yet work in a repeat...-->
                                     </options>
                                     <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
                                 </param>
@@ -358,24 +412,39 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="replicates_counts" format="tabular" label="${tool.name} replicates counts on ${on_string}"/>
-        <data name="all_events_table" format="tabular" label="${tool.name} all events table on ${on_string}"/>
-        <data name="experiment_events" format="tabular" label="${tool.name} experiment events on ${on_string}"/>
-        <data name="output_html" format="html" label="${tool.name} on ${on_string}"/>
+        <data name="output_design_file" format="tabular" label="${tool.name} (design file) on ${on_string}">
+            <filter>save_design_file == 'yes'</filter>
+        </data>
+        <data name="output_bed" format="bed" label="${tool.name} (bed) on ${on_string}"/>
+        <data name="output_html" format="html" label="${tool.name} (html) on ${on_string}"/>
+        <data name="replicates_counts" format="tabular" label="${tool.name} (replicates counts) on ${on_string}"/>
+        <data name="all_events_table" format="tabular" label="${tool.name} (all events table) on ${on_string}"/>
     </outputs>
     <tests>
         <test>
-            <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
-            <param name="advanced_options_cond" value="hide" />
-            <output name="output_html" file="hg19_output_html1.html" ftype="html" lines_diff="12"/>
+            <repeat name="condition_repeat">
+                <repeat name="signal_repeat">
+                    <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
+                </repeat>
+            </repeat>
+            <param name="advanced_options" value="hide" />
+            <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/>
+            <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/>
             <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="hg19" />
-            <param name="ctrl" value="cntrl_hg19.scidx" ftype="bam" dbkey="hg19" />
-            <param name="advanced_options_cond" value="display" />
-            <output name="output_html" file="hg19_output_html2.html" ftype="html" lines_diff="12"/>
+            <repeat name="condition_repeat">
+                <repeat name="signal_repeat">
+                    <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
+                </repeat>
+                <repeat name="control_repeat">
+                    <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />
+                </repeat>
+            </repeat>
+            <param name="advanced_options" value="display" />
+            <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/>
+            <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/>
             <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>
@@ -387,8 +456,9 @@
 MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing
 differential binding events between conditions.  MultiGPS encourages consistency in the reported binding
 event locations across conditions and provides accurate estimation of ChIP enrichment levels at each event.
-MultiGPS loads all data to memory, so you will need a lot of available memory if you are running analysis
-over many conditions or large datasets.
+MultiGPS performs significant EM optimization of binding events along the genome and across experimental
+conditions, and it integrates motif-finding via MEME.  The tool loads all data into memory, so the potential
+exists for time and memory intensive analyses if running over many conditions or large datasets.
 
 -----
 
@@ -396,7 +466,7 @@
 
 * **Loading data:**
 
- - **Optional file containing reads from a control experiment** - must be same format as input experiment
+ - **Optional file containing reads from a control experiment** - file containing reads from a control 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.
@@ -450,6 +520,23 @@
 
     </help>
     <citations>
-        <citation type="doi">10.1371/journal.pcbi.1003501</citation>
+        <citation type="bibtex">
+            @article{Mahony2014,
+            journal = {PLOS Computational Biology},
+            author = {1. Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK},
+            title = {An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding},
+            year = {2014},}
+            volume = {10},
+            number = {3},
+            pages = {e1003501},}
+        </citation>
+        <citation type="bibtex">
+            @article{Liang2012,
+            journal = {BMC Bioinformatics},
+            author = {2. Liang, Ketes},
+            title = {Normalization of ChIP-seq data with control},
+            year = {2012},}
+        </citation>
     </citations>
 </tool>
+