diff checkSnpEffCandidates.xml @ 0:a3873bb68495

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/checkSnpEffCandidates.xml	Tue Mar 20 11:02:34 2012 -0400
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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
+
+------
+
+**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
+
+
+------
+
+**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>