annotate checkSnpEffCandidates.xml @ 9:f20585ccbf05 draft default tip

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<tool id="check_snpeff_candidates" name="CloudMap: 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 CloudMap Galaxy page:

http://usegalaxy.org/cloudmap


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**Citation:**

This tool is part of the CloudMap pipeline for analysis of mutant genome sequences. For further details, please see `Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, and Oliver Hobert.  CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (Genetics 2012 In Press)`__

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

Correspondence to [e-mail] (G.M.) or [e-mail] (O.H.)
    </help>
</tool>