diff fathmm/fathmm.xml @ 0:fd66648ce5f9 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fathmm/fathmm.xml	Tue Oct 07 19:25:07 2014 -0400
@@ -0,0 +1,65 @@
+<tool id="fathmm_web" name="FATHMM">
+    <description>fathmm web service</description>
+    <requirements>
+        <requirement type="package" version="2.2.1">requests</requirement>
+        <requirement type="python-module">requests</requirement>
+    </requirements>
+    <command interpreter="python">fathmm.py --input $input --output $output --threshold $threshold
+    </command>
+    <inputs>
+        <param name="input" format="txt" type="data" label="Input variants" />
+        <param name="threshold" type="float" label="Threshold cutoff" value="-0.75" help="Predictions with scores less than this indicate that the mutation is potentially associated with cancer" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fathmm_input.txt"/>
+            <param name="threshold" value="-0.75" />
+            <output name="output" file="fathmm_output.tab" lines_diff="2"/>
+        </test>
+    </tests>
+    <help>
+
+
+    **What it does**
+
+
+        This script calls FATHMM(http://supfam3.cs.bris.ac.uk/FATHMM/about.html) Web API to fetch
+        predict functional impact of mutations.
+
+        Input is a plain text file:
+
+        1.  &lt;protein&gt;  &lt;substitution&gt;
+
+        2.  dbSNP rs identifiers
+
+
+        Where &lt;protein&gt;  is the protein identifier and
+        &lt;substitution&gt; is the amino acid substitution in the conventional one letter format.
+        Multiple substitutions can be entered on a single line and should be separated by a comma.
+        SwissProt/TrEMBL, RefSeq and Ensembl protein identifiers are accepted:
+
+        P43026 L441P
+        ENSP00000325527 N548I,E1073K,C2307S
+
+
+
+    **Citations**
+
+        If you use this tool in Galaxy, please cite :
+
+        Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GLA, Edwards KJ, Day INM, Gaunt, TR. (2013).
+        Predicting the Functional, Molecular and PhenotypicConsequences of Amino Acid Substitutions using
+        Hidden Markov Models. Hum. Mutat., 34:57-65
+
+        Shihab HA, Gough J, Cooper DN, Day INM, Gaunt, TR. (2013). Predicting the Functional Consequences
+        of Cancer-Associated Amino Acid Substitutions. Bioinformatics 29:1504-1510.
+
+        Shihab HA, Gough J, Mort M, Cooper DN, Day INM, Gaunt, TR. (2014).
+        Ranking Non-Synonymous Single Nucleotide Polymorphisms based on Disease Concepts. In Press
+
+    </help>
+</tool>
+