<?xml version="1.0"?>
<tool id="genetrack" name="GeneTrack" version="@WRAPPER_VERSION@.0">
    <description>peak predictor</description>
    <macros>
        <import>genetrack_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
        python $__tool_directory__/genetrack.py
        --input_format $input_format_cond.input_format
        #if str($input_format_cond.input_format) == "scidx":
            #for $i in $input_format_cond.input_scidx:
                 --input "${i}" "${i.hid}"
            #end for
        #elif str($input_format_cond.input_format) == "gff":
            #for $i in $input_format_cond.input_gff:
                 --input "${i}" "${i.hid}"
            #end for
        #end if
        --sigma $sigma
        --exclusion $exclusion
        --up_width $up_width
        --down_width $down_width
        --filter $filter
    </command>
    <inputs>
        <conditional name="input_format_cond">
            <param name="input_format" type="select" label="Format of files for conversion">
                <option value="scidx" selected="True">ScIdx</option>
                <option value="gff">Gff</option>
            </param>
            <when value="scidx">
                <param name="input_scidx" type="data" format="scidx" multiple="True" label="Predict peaks on" />
            </when>
            <when value="gff">
                <param  name="input_gff" type="data" format="gff" multiple="True" label="Predict peaks on" />
            </when>
        </conditional>
        <param name="sigma" type="integer" value="5" min="1" label="Sigma to use when smoothing reads" help="Higher values increase computation but produce more smoothing." />
        <param name="exclusion" type="integer" value="20" min="1" label="Peak exclusion zone" help="Exclusion zone around each peak that prevents others from being called." />
        <param name="up_width" type="integer" value="10" min="0" label="Upstream width of called peaks" />
        <param name="down_width" type="integer" value="10" min="0" label="Downstream width of called peaks" />
        <param name="filter" type="integer" value="3" min="0" label="Absolute read filter" help="Removes peaks with lower peak height." />
    </inputs>
    <outputs>
        <collection name="genetrack_output" type="list" label="Genetrack results on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input_gff" value="genetrack_input2.gff" ftype="gff" />
            <param name="input_format" value="gff" />
            <param name="sigma" value="5" />
            <param name="exclusion" value="20" />
            <param name="up_width" value="10" />
            <param name="down_width" value="10" />
            <param name="filter" value="3" />
            <output_collection name="genetrack_output" type="list">
                <element name="s5e20u10d10F3_on_data_1" file="genetrack_output2.gff" ftype="gff" />
            </output_collection>
        </test>
        <test>
            <param name="input_scidx" value="genetrack_input3.scidx" ftype="scidx" />
            <param name="input_format" value="scidx" />
            <param name="sigma" value="5" />
            <param name="exclusion" value="20" />
            <param name="up_width" value="10" />
            <param name="down_width" value="10" />
            <param name="filter" value="3" />
            <output_collection name="genetrack_output" type="list">
                <element name="s5e20u10d10F3_on_data_1" file="genetrack_output3.gff" ftype="gff" />
            </output_collection>
        </test>
        <test>
            <param name="input_gff" value="genetrack_input_unsorted4.gff" ftype="gff" />
            <param name="input_format" value="gff" />
            <param name="sigma" value="5" />
            <param name="exclusion" value="20" />
            <param name="up_width" value="10" />
            <param name="down_width" value="10" />
            <param name="filter" value="3" />
            <output_collection name="genetrack_output" type="list">
                <element name="s5e20u10d10F3_on_data_1" file="genetrack_output4.gff" ftype="gff" />
            </output_collection>
        </test>
    </tests>
    <help>
**What it does**

Genetrack supports ChIP experiments.  The peak caller takes a standard set of data on both the sense and
antisense strands (ScIdx format) and smooths their relative reads. It then predicts the peaks present in
the smoothed dataset and uses those peak locations to find the maximal non-overlapping subset.  It then
selects the highest peak and establishes an exclusion zone, and no other predicted peaks will be reported
within the exclusion zone.  Finally, it ensures each peak is above a threshold and that two peaks are not
too close to each other.

-----

**Options**

* **Sigma to use when smoothing reads** - Sigma to use when smoothing reads to call peaks.
* **Peak exclusion zone** - Exclusion zone around each peak that prevents others from being called.
* **Upstream width of called peaks** - Upstream width of called peaks.
* **Downstream width of called peaks** - Downstream width of called peaks.
* **Filter** - Absolute read filter.  Restricts output to only peaks with larger peak height.
    </help>
    <expand macro="citations" />
</tool>