--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/multigps.xml	Wed Dec 23 10:08:24 2015 -0500
@@ -0,0 +1,141 @@
+<tool id="multigps" name="MultiGPS" version="0.5.0.0">
+    <description>analyzes collections of multi-condition ChIP-seq data</description>
+    <requirements>
+        <requirement type="package" version="4.11.0">meme</requirement>
+        <requirement type="package" version="3.11.0">edger</requirement>
+        <requirement type="package" version="2.14">biocbasics</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+            ## when I don't run on my mac...
+            ## java -Xmx20G -jar $__tool_directory__/multigps_v0.5.jar
+            mkdir multigps_out &&
+            java -jar $__tool_directory__/multigps_v0.5.jar
+            --threads="\${GALAXY_SLOTS:-4}"
+            --verbose
+            --geninfo ${chromInfo}
+            #if str($use_motif_cond.use_motif) == "yes":
+                #set seq_dir = python "$get_seq_dir"
+                --seq "${seq_dir}"
+                --mememinw $use_motif_cond.min_motif_width
+                --mememaxw $use_motif_cond.max_motif_width
+            --design $design_file
+            #if str($gauss_model_smoothing_cond.gauss_model_smoothing) == "yes":
+                --gaussmodelsmoothing
+                --gausssmoothparam $gauss_model_smoothing_cond.gauss_model_smoothing.gauss_smooth
+            #end if
+            --out multigps_out
+        ]]>
+    </command>
+    <configfiles>
+        <configfile name="design_file">
+            <![CDATA[
+            #for input in $input_files:
+                #set filename = "{$input['input'].filename}"
+                #set signal_control = $input['signal_control']
+                #set format = $input['input'].ext
+                #set condition_name = $input['condition_name']
+                #set replicate_name = $input['replicate_name']
+                #set line = '\t'.join($filename, $signal_control, $format, $condition_name, $replicate_name])
+                ${line}
+            #end for
+            ]]>
+        </configfile>
+        <configfile name="get_seq_dir">
+<![CDATA[
+#!/usr/bin/env python
+import os
+import tempfile
+
+# All inputs must have the same dbkey, and MultiGPS requires a directory, not the reference file.
+if $use_motif_cond.reference_genome_cond.reference_genome_source == "cached":
+    return os.path.split($use_motif_cond.reference_genome_cond.reference_genome.fields.path)[0]
+else:
+    seq_dir = tempfile.mkdtemp(prefix="tmp-multigps-")
+    # Populate the directory with the history dataset
+    tmp_filename = "%s.fa" % $use_motif_cond.reference_genome_cond.reference_genome.dbkey
+    ln -f -s $use_motif_cond.reference_genome_cond.reference_genome.filename os.path.join(seq_dir, tmp_filename)
+    return seq_dir
+]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <repeat name="input_files" title="Input Files" min="1">
+            <param name="input" type="data" format="bam,bed,scidx" label="Add file">
+                <validator type="unspecified_build" />
+            </param>
+            <param name="signal_control" type="select" label="Signal or control" display="checkboxes" >
+                <option value="signal" selected="True">Signal</option>
+                <option value="control">Control</option>
+            </param>
+            <param label="Condition name" name="condition_name" type="text" />
+            <param label="Replicate name" name="replicate_name" type="text" />
+
+            <conditional name="use_motif_cond">
+                <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?">
+                    <option value="yes" selected="True">Yes</option>
+                    <option value="no">No</option>
+                </param>
+                <when value="yes">
+                    <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>
+                            <option value="history">From History</option>
+                        </param>
+                        <when value="cached">
+                            <param name="reference_genome" type="select" label="Using reference genome">
+                                <options from_data_table="fasta_indexes"/>
+                                <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                            </param>
+                        </when>
+                        <when value="history">
+                            <param name="reference_genome" type="data" format="fasta" label="Using reference genome"/>
+                        </when>
+                    </conditional>
+                    <param name="min_motif_width" type="integer" min="0" value="6" label="Minimum motif width for MEME">
+                    <param name="max_motif_width" type="integer" min="0" value="16" label="Maximum motif width for MEME">
+                </when>
+                <when value="no">
+            </conditional>
+
+
+        </repeat>
+
+        <param name="genome_info_file" type="data" format="tabular" label="Genome information dataset" help="What's this?  See the help section below."/>
+        <conditional name="gauss_model_smoothing_cond">
+            <param  name="gauss_model_smoothing" type="select" label="Turn on Gaussian model smoothing?" help="Smoothing is done with a cubic spline.">
+                <option value="yes" selected="True">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param name="gauss_smooth" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." />
+            </when>
+            <when value="no" />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_report" format="txt" label="MultiGPS-Report"/>
+        <data name="output_gff" format="gff" label="MultiGPS-GFF" />
+        <data name="output_gz" format="gz" label="MultiGPS-GZ" />
+    </outputs>
+    <help>
+
+**What it does**
+
+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.
+
+-----
+
+**Options**
+
+* **Input Files**
+
+    </help>
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1003501</citation>
+    </citations>
+</tool>