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<tool id="peptide_genomic_coordinate" name="Peptide Genomic Coodinate" version="0.1.1">
    <description>Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB</description>
    <requirements>
        <requirement type="package" version="3.7.1">python</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        python '$__tool_directory__/peptide_genomic_coordinate.py' 
        '$peptideinput'
        '$mzsqlite'
        '$mapping'
        '$peptide_bed'
    ]]></command>
    <inputs>
        <param type="data" name="peptideinput" format="tabular" label="Peptide List (without any header line)"/>
        <param type="data" name="mzsqlite" format="sqlite" label="mz to sqlite (mzsqlite) file"/>
        <param type="data" name="mapping" format="sqlite" label="genomic mapping sqlite file"/>
    </inputs>
    <outputs>
        <data format="bed" name="peptide_bed" label="${tool.name} on ${on_string}">
            <actions>
                <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="peptideinput" value="peptides.tabular"/>
            <param name="mzsqlite" value="test_mz_to_sqlite.sqlite"/>
            <param name="mapping" value="test_genomic_mapping_sqlite.sqlite"/>
            <output name="peptide_bed">
                <assert_contents>
                    <has_text text="115176449" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        **Peptide Genomic Coodinate**

        Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files. This tool is useful in a proteogenomics workflow.
        This program loads two sqlite databases (mzsqlite and genomic mapping sqlite files) and calculates the genomic coordinates of the peptides provided as input. This outputs bed file for peptides.
    
        Input: Peptide list file, mzsqlite sqlite DB file, and genomic mapping sqlite DB file 
        Output: Tabular BED file with all the columns
        
        

    ]]></help>
    <citations>
      <citation type="bibtex">
@misc{peptidegenomiccoodinate,
    author={Kumar, Praveen},
    year={2018},
    title={Peptide Genomic Coordinate}
}
      </citation>
    </citations>
</tool>