comparison pep_pointer.xml @ 0:032f1ee171ed draft

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0:032f1ee171ed

<tool id="pep_pointer" name="PepPointer: classify genomic location of peptides" version="0.1.0">
    <requirements>
        <requirement type="package" version="2.7.9">python</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        python '$__tool_directory__/pep_pointer.py' '$gtf' '$bed' '$classified'
    ]]></command>
    <inputs>
        <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
        <param type="data" name="bed" format="bed" label="BED file with chromosomal coordinates of peptide"/>
    </inputs>
    <outputs>
        <data format="tabular" name="classified"/>
    </outputs>
    <tests>
        <test>
            <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>