Mercurial > repos > saket-choudhary > fathmm_web
comparison 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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-1:000000000000 | 0:fd66648ce5f9 |
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1 <tool id="fathmm_web" name="FATHMM"> | |
2 <description>fathmm web service</description> | |
3 <requirements> | |
4 <requirement type="package" version="2.2.1">requests</requirement> | |
5 <requirement type="python-module">requests</requirement> | |
6 </requirements> | |
7 <command interpreter="python">fathmm.py --input $input --output $output --threshold $threshold | |
8 </command> | |
9 <inputs> | |
10 <param name="input" format="txt" type="data" label="Input variants" /> | |
11 <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" /> | |
12 </inputs> | |
13 <outputs> | |
14 <data name="output" format="tabular"/> | |
15 </outputs> | |
16 <tests> | |
17 <test> | |
18 <param name="input" value="fathmm_input.txt"/> | |
19 <param name="threshold" value="-0.75" /> | |
20 <output name="output" file="fathmm_output.tab" lines_diff="2"/> | |
21 </test> | |
22 </tests> | |
23 <help> | |
24 | |
25 | |
26 **What it does** | |
27 | |
28 | |
29 This script calls FATHMM(http://supfam3.cs.bris.ac.uk/FATHMM/about.html) Web API to fetch | |
30 predict functional impact of mutations. | |
31 | |
32 Input is a plain text file: | |
33 | |
34 1. <protein> <substitution> | |
35 | |
36 2. dbSNP rs identifiers | |
37 | |
38 | |
39 Where <protein> is the protein identifier and | |
40 <substitution> is the amino acid substitution in the conventional one letter format. | |
41 Multiple substitutions can be entered on a single line and should be separated by a comma. | |
42 SwissProt/TrEMBL, RefSeq and Ensembl protein identifiers are accepted: | |
43 | |
44 P43026 L441P | |
45 ENSP00000325527 N548I,E1073K,C2307S | |
46 | |
47 | |
48 | |
49 **Citations** | |
50 | |
51 If you use this tool in Galaxy, please cite : | |
52 | |
53 Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GLA, Edwards KJ, Day INM, Gaunt, TR. (2013). | |
54 Predicting the Functional, Molecular and PhenotypicConsequences of Amino Acid Substitutions using | |
55 Hidden Markov Models. Hum. Mutat., 34:57-65 | |
56 | |
57 Shihab HA, Gough J, Cooper DN, Day INM, Gaunt, TR. (2013). Predicting the Functional Consequences | |
58 of Cancer-Associated Amino Acid Substitutions. Bioinformatics 29:1504-1510. | |
59 | |
60 Shihab HA, Gough J, Mort M, Cooper DN, Day INM, Gaunt, TR. (2014). | |
61 Ranking Non-Synonymous Single Nucleotide Polymorphisms based on Disease Concepts. In Press | |
62 | |
63 </help> | |
64 </tool> | |
65 |