<tool id="filter_combined_via_tracking" name="Filter Combined Transcripts" version="0.1">
    <description>using tracking file</description>
    <command interpreter="python">
        filter_transcripts_via_tracking.py 
            $tracking_file
            $transcripts_file
            $filtered_transcripts
            $sample_num
    </command>
    <inputs>
        <param format="gtf" name="transcripts_file" type="data" label="Cufflinks assembled transcripts" help=""/>
        <param format="tabular" name="tracking_file" type="data" label="Cuffcompare tracking file" help=""/>
        <param name="sample_num" type="select" label="Sample Number">
            <option value="1">1</option>
            <option value="2">2</option>
        </param>
    </inputs>

    <outputs>
        <data format="gtf" name="filtered_transcripts"/>
    </outputs>

    <tests>
    </tests>

    <help>
        Uses a tracking file (produced by cuffcompare) to filter a GTF file of transcripts (usually the transcripts produced by 
        cufflinks). Filtering is done by extracting transcript IDs from tracking file and then filtering the 
        GTF so that the output GTF contains only transcript found in the tracking file. Because a tracking file has multiple 
        samples, a sample number is used to filter transcripts for a particular sample.
    </help>
</tool>