<tool id="pep_pointer" name="PepPointer" version="0.1.1">
    <description>classify genomic location of peptides</description>
    <requirements>
        <requirement type="package" version="2.7.9">python</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf' '$bed' '$classified'
    ]]></command>
    <inputs>
        <conditional name="gtf_input">
            <param type="select" name="gtf_source" label="Choose the source of the GTF file">
                <option value="cached" selected="true">Built-in</option>
                <option value="history">From history</option>
            </param>
            <when value="cached">
                <param name="gtf" type="select" format="gtf" label="GTF file with the genome of interest">
                    <options from_data_table="pep_pointer"/>
                </param>
            </when>
            <when value="history">
                <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
            </when>
        </conditional>
        <param type="data" name="bed" format="bed" label="BED file with chromosomal coordinates of peptide"/>
    </inputs>
    <outputs>
        <data format="tabular" name="classified" label="${tool.name} on ${on_string}">
            <actions>
                <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,annotation"/>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="gtf_source" value="history"/>
            <param name="gtf" value="mus17.gtf"/>
            <param name="bed" value="novel_peptides_17.bed"/>
            <output name="classified" file="classified_novel_peptides.txt"/>
        </test>
    </tests>
    <help><![CDATA[
        **PepPointer**

        Given chromosomal locations of peptides in a BED file, PepPointer classifies them as CDS, UTR, exon, intron, or intergene. 
    ]]></help>
    <citations>
      <citation type="bibtex">
@misc{peppointer,
    author={Kumar, Praveen},
    year={2017},
    title={PepPointer}
}
      </citation>
    </citations>
</tool>