Mercurial > repos > saket-choudhary > fathmm_web
diff fathmm/fathmm.xml @ 0:fd66648ce5f9 draft default tip
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author | saket-choudhary |
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date | Tue, 07 Oct 2014 19:25:07 -0400 |
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--- /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. <protein> <substitution> + + 2. dbSNP rs identifiers + + + Where <protein> is the protein identifier and + <substitution> 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> +