Mercurial > repos > gregory-minevich > check_snpeff_candidates
changeset 8:f5a8d626a329 draft
Uploaded
| author | gregory-minevich |
|---|---|
| date | Mon, 08 Oct 2012 16:14:27 -0400 |
| parents | 4d4da4864c56 |
| children | f20585ccbf05 |
| files | checkSnpEffCandidates.xml |
| diffstat | 1 files changed, 51 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/checkSnpEffCandidates.xml Mon Oct 08 16:14:27 2012 -0400 @@ -0,0 +1,51 @@ +<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 + +------ + +**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 + + +------ + +**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 gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.) + </help> +</tool>