<tool id="Nucleosome" name="Nucleosome Predictions" version="3.0">
    <xrefs>
        <xref type="bio.tools">nucleosome_prediction</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="3.0">nucleosome_prediction</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      nucleosome_prediction.pl
        -t Example
        -s '$input'
        -p predition_output
        -tab
        -c $c
        -temp $temp
        $raw_binding
    ]]></command>

    <inputs>
        <param type="data" name="input" label="Input sequence file (.fasta format)" format="fasta" />
        <param argument="-c" type="float" value="0.1"
            label="Nucleosomes Concentration" help="Nucleosomes concentration: the default value = 0.1"/>
        <param argument="-temp" type="integer" value="1"
            label="Temperature Scaling" help="Temperature scaling: the default value = 1"/>
        <param argument="-raw_binding" type="boolean" truevalue="-raw_binding" falsevalue=""
            label="Raw Binding" help="Raw Binding: When 'No' (default), then the output will be the default average occupancy probabilities. When 'yes', then the output will be  the raw nucleosome binding log-ratio per basepair"/>
    </inputs>

    <outputs>
        <data name="output" format="tabular" from_work_dir="predition_output.tab" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="input.fa" ftype="fasta"/>
            <param name="raw_binding" value="True"/>
            <output name="output" file="npresults.tab" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="input.fa" ftype="fasta"/>
            <param name="c" value="0.1"/>
            <param name="temp" value="1"/>
            <output name="output" file="npresultsf.tab" ftype="tabular"/>
        </test>
    </tests>

    <help><![CDATA[

    **What it does**
    This tool allows you to submit a genomic sequence and to recieve a prediction of the nucleosomes positions on it, based on the nucleosome-DNA interaction model that we developed in these papers:
    This version (version 3) is applicable to all species.

    The tool takes a sequence .fasta file and finds all positions of the matrices above the background

    ]]></help>

    <citations>

        <citation type="bibtex">
          @MISC{10.1038/nature07667,
                      DOI = {10.1038/nature07667},
                      note = {The DNA-encoded nucleosome organization of a eukaryotic genome}
                      year = "2009"
                  }
        </citation>
    </citations>

</tool>