diff tools/condel/condel_web.xml @ 0:742c7ee37f8b

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+++ b/tools/condel/condel_web.xml	Wed Nov 20 00:48:30 2013 +0530
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+<tool id="condel_web" name="condel">
+    <description>Condel web service</description>
+    <command interpreter="python">
+        condel_web.py --input $input --output $output
+    </command>
+    <inputs>
+        <param name="input" format="text" type="data" label="Input Variants" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <help>
+        **What it does**
+        Condel stands for CONsensus DELeteriousness score of non-synonymous single nucleotide variants (SNVs).
+        The idea behind it is to integrate the output of computational tools aimed at assessing the impact of non synonymous
+        SNVs on protein function. To do this, it computes a weighted average of the scores (WAS) of these tools.
+        Condel was developed to integrate the outputs of five tools: SIFT, Polyphen2, MAPP, LogR Pfam E-value
+        (implemented ad hoc following the instructions at Clifford RJ, Edmonson MN, Nguyen C, and Buetow KH (2004)
+        Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. Bioinformatics 20, 1006-1014) and MutationAssessor
+
+
+        The scores of different methods are weighted using the complementary cumulative distributions produced by the five
+        methods on a dataset of approximately 20000 missense SNPs, both deleterious and neutral.
+        The probability that a predicted deleterious mutation is not a false positive of the method and the probability that a
+        predicted neutral mutation is not a false negative are employed as weights
+
+        **Citation**
+
+        If you use this Galaxy tool in work leading to a scientific publication please cite:
+
+        Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score,
+        Condel (2011) Abel González-Pérez and Nuria López-Bigas, American Journal of Human Genetics 10.1016/j.ajhg.2011.03.004
+    </help>
+</tool>
+