--- a/multigps.xml	Tue Dec 13 13:20:28 2016 -0500
+++ b/multigps.xml	Tue Dec 13 14:49:54 2016 -0500
@@ -3,16 +3,20 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <requirements>
+        <requirement type="package" version="0.72">multigps</requirement>
+    </requirements>
     <command detect_errors="aggressive">
-    <command>
         <![CDATA[
             multigps
             ############################
             ## General options
             ############################
-            --input "$input"
-            --format "$input.ext"
+            --expt "$expt"
+            --format "$expt.ext"
+            #if len($ctrl) > 0:
+                --ctrl "$ctrl"
+            #end if
             #if str($verbose) == 'yes':
                 --verbose
             #end if
@@ -21,25 +25,28 @@
             ## Advanced options
             ############################
             #set aoc = $advanced_options_cond
-            #if str($aoc.advanced_options) == "display":
+            #if str($aoc.advanced_options) == 'display':
                 #set bmsc = $aoc.binding_model_smoothing_cond
                 #set gmsc = $aoc.gauss_model_smoothing_cond
                 #set rbec = $aoc.report_binding_events_cond
                 #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 rgc = $umc.reference_genome_cond
                 ############################
                 ## Limits on how many reads
                 ############################
-                #if str($rloc.reads_limits) == "yes":
+                #if str($rloc.reads_limits) == 'yes':
                     --fixedpb $rloc.fixedpb
                     --poissongausspb $rloc.poissongausspb
-                    #if str($rloc.nonunique) == "yes":
+                    #if str($rloc.nonunique) == 'yes':
                         --nonunique
                     #end if
                     --mappability $rloc.mappability
                 #end if
-                #if str($rloc.nocache) == "yes":
+                #if str($rloc.nocache) == 'yes':
                     --nocache
                 #end if
                 ############################
@@ -100,7 +107,6 @@
                 ## MultiGPS priors
                 ############################
                 #if str($umc.use_motif) == 'yes':
-                    #set rgc = $umc.reference_genome_cond
                     #if str($rgc.reference_genome_source) == "cached":
                         #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0]
                     #else:
@@ -113,11 +119,9 @@
                         #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename)
                         ln -f -s $tmp_seq_file $seq_file &&
                     #end if
-                    #set mpc = $umc.multigps_priors_cond
                     --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
@@ -153,15 +157,13 @@
             #end if
             --out "$output_html.files_path"
             > "$output_html"
-            ##if str($output_process_log) == 'yes':
-            ##    --output_process_path "$output_process"
-            ###end if
         ]]>
     </command>
     <inputs>
-        <param name="input" type="data" format="bam,bed,scidx" label="Add input file" help="Supported formats are bam, bed and scidx">
+        <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="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>
@@ -278,7 +280,7 @@
                     <option value="yes" selected="True">Yes</option>
                     <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." />
+                <param name="exclude" type="data" optional="True" format="tabular" 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
@@ -303,7 +305,7 @@
                             <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="input" column="1"/>
+                                        <filter type="data_meta" key="dbkey" ref="expt" column="1"/>
                                     </options>
                                     <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                                 </param>
@@ -311,7 +313,7 @@
                             <when value="history">
                                 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
                                     <options>
-                                        <filter type="data_meta" key="dbkey" ref="input"/>
+                                        <filter type="data_meta" key="dbkey" ref="expt"/>
                                     </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>
@@ -383,7 +385,7 @@
                     </when>
                 </conditional>
             </when>
-            <when value="hide"/>
+            <when value="hide" />
         </conditional>
         <!--
         <param name="output_process_log" type="select" label="Output MultiGPS process log?">
@@ -393,16 +395,11 @@
         -->
     </inputs>
     <outputs>
-        <!--
-        <data name="output_process" format="txt" label="${tool.name} on ${on_string} (process log)">
-            <filter>output_process_log == "yes"</filter>
-        </data>
-        -->
         <data name="output_html" format="html"/>
     </outputs>
     <tests>
         <test>
-            <param name="input" value="sacCer3_1.scidx" ftype="scidx" dbkey="sacCer3"/>
+            <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"/>