<tool id="fimo_gff_to_gff" name="Fimo Gff to Gff" version="1.0.0">
    <description></description>
    <requirements>
        <requirement type="package" version="5.18.1">perl</requirement>
    </requirements>
    <command>
        <![CDATA[
            mkdir -p output &&
            perl $__tool_directory__/fimo_gff_to_gff.pl "$input" output
        ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="tabular" label="FIMO (almost) Gff input" />
    </inputs>
    <outputs>
        <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="input.tabular" ftype="tabular" />
            <output_collection name="motifs" type="list">
                <element name="MOTIF1" file="motif1.gff" ftype="gff"/>
            </output_collection>
        </test>
    </tests>
    <help>

.. class:: warningmark

This tool requires 1-based input data, 0-based data will produce incorrect results.

.. class:: warningmark

This tool requires FASTA headers that use the default bedtools getfasta header format of
**chrom:start-stop(strand)** or **chrom:start-stop** in which case strand is set as '+'
per the bedtools standard.

**What it does**

Converts FIMO tabular (almost GFF) files to true genomic coordinates in valid GFF format.  A
collection of datasets is produced consisting of one dataset per motif discovered in the input.

    </help>
    <citations>
        <citation type="bibtex">
            @unpublished{None,
            author = {Lai, William},
            title = {None},
            year = {None},
            eprint = {None},
            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
        }</citation>
    </citations>
</tool>