<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[
            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>