--- /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>