annotate checkSnpEffCandidates.xml @ 0:a3873bb68495

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<tool id="check_snpeff_candidates" name="Check snpEff Candidates">
    <description>Marks up a snpEff output file with matches to a gene candidate list.</description>
    <command interpreter="python">checkSnpEffCandidates.py -s $snpeff_file -c $candidate_list -o $output</command>
    <inputs>
        <param name="snpeff_file" type="data" format="tabular" label="SnpEff File" help="tabular output file from snpEff"/>
        <param name="candidate_list" type="data" format="tabular" label="Candidate List" help="2 column list consisting of candidate genes and a description"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" />
    </outputs>
    <requirements>
        <requirement type="python-module">sys</requirement>
        <requirement type="python-module">optparse</requirement>
        <requirement type="python-module">csv</requirement>
    </requirements>
    <tests>
	<param name="snpeff_file" value="" />
	<param name="candidate_list" value="" />
    </tests>
    <help>

**What it does:** 

Indicates on a SnpEff output file which genes are found in a candidate list by comparing Gene IDs.  

For a description of the snpEff variant annotation and effect prediction tool:

http://snpeff.sourceforge.net

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**Input:** 

The candidate list should be in a tabular format with two columns: Gene ID and Gene Description (e.g. C55B7.12 and transcription_factor). The file should contain no headers.

Useful candidate lists (e.g. transcription factors, genes expressed in neurons, transgene silencers, chromatin factors) are available on the Hobert Lab website:

http://biochemistry.hs.columbia.edu/labs/hobert/literature.html


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**Citation:**

This tool is part of the CloudMap package from the Hobert Lab. If you use this tool, please cite `Gregory Minevich, Danny Park, Richard J. Poole and Oliver Hobert CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (2012 In Preparation)`__

    .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html


    </help>
</tool>