Mercurial > repos > devteam > filter_transcripts_via_tracking

<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>
        **What it does**

        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>
author	devteam
date	Tue, 13 Oct 2015 12:21:22 -0400
parents	0601d9a817c7
children