Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/wolf_psort.xml @ 5:0f1c61998b22
Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 18:06:27 -0400 |
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children | a290c6d4e658 |
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1 <tool id="wolf_psort" name="WoLF PSORT" version="0.0.1"> | |
2 <description>Eukaryote protein subcellular localization prediction</description> | |
3 <command interpreter="python"> | |
4 wolf_psort.py $organism 8 $fasta_file $tabular_file | |
5 ##I want the number of threads to be a Galaxy config option... | |
6 </command> | |
7 <inputs> | |
8 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> | |
9 <param name="organism" type="select" display="radio" label="Organism"> | |
10 <option value="animal">Animal</option> | |
11 <option value="plant">Plant</option> | |
12 <option value="fungi">Fungi</option> | |
13 </param> | |
14 </inputs> | |
15 <outputs> | |
16 <data name="tabular_file" format="tabular" label="WoLF PSORT $organism results" /> | |
17 </outputs> | |
18 <requirements> | |
19 <requirement type="binary">runWolfPsortSummary</requirement> | |
20 </requirements> | |
21 <help> | |
22 | |
23 **What it does** | |
24 | |
25 This calls the WoLF PSORT tool for prediction of eukaryote protein subcellular localization. | |
26 | |
27 The input is a FASTA file of protein sequences, and the output is tabular with four columns (multiple rows per protein): | |
28 | |
29 * Sequence identifier | |
30 * Compartment | |
31 * Score | |
32 * Prediction rank | |
33 | |
34 | |
35 **Localization Compartments** | |
36 | |
37 The table below gives the WoLF PSORT localization site definitions, and the corresponding Gene Ontology (GO) term. | |
38 | |
39 ====== ===================== ===================== | |
40 Abbrev Localization Site GO Cellular Component | |
41 ------ --------------------- --------------------- | |
42 chlo chloroplast 0009507, 0009543 | |
43 cyto cytosol 0005829 | |
44 cysk cytoskeleton 0005856(2) | |
45 E.R. endoplasmic reticulum 0005783 | |
46 extr extracellular 0005576, 0005618 | |
47 golg Golgi apparatus 0005794(1) | |
48 lyso lysosome 0005764 | |
49 mito mitochondria 0005739 | |
50 nucl nuclear 0005634 | |
51 pero peroxisome 0005777(2) | |
52 plas plasma membrane 0005886 | |
53 vacu vacuolar membrane 0005774(2) | |
54 ====== ===================== ===================== | |
55 | |
56 Additionally compound predictions like mito_nucl are also given. | |
57 | |
58 | |
59 **Notes** | |
60 | |
61 The raw output from WoLF PSORT looks like this (space separated), showing two proteins: | |
62 | |
63 ================================ ============================================ | |
64 gi|301087619|ref|XP_002894699.1| extr 12, mito 4, E.R. 3, golg 3, mito_nucl 3 | |
65 gi|301087623|ref|XP_002894700.1| extr 21, mito 2, cyto 2, cyto_mito 2 | |
66 ================================ ============================================ | |
67 | |
68 This is reformatted into a tabular file as follows for use in Galaxy: | |
69 | |
70 ================================ =========== ===== ==== | |
71 #ID Compartment Score Rank | |
72 -------------------------------- ----------- ----- ---- | |
73 gi|301087619|ref|XP_002894699.1| extr 12 1 | |
74 gi|301087619|ref|XP_002894699.1| mito 4 2 | |
75 gi|301087619|ref|XP_002894699.1| E.R. 3 3 | |
76 gi|301087619|ref|XP_002894699.1| golg 3 4 | |
77 gi|301087619|ref|XP_002894699.1| mito_nucl 3 5 | |
78 gi|301087623|ref|XP_002894700.1| extr 21 1 | |
79 gi|301087623|ref|XP_002894700.1| mito 2 2 | |
80 gi|301087623|ref|XP_002894700.1| cyto 2 3 | |
81 gi|301087623|ref|XP_002894700.1| cyto_mito 2 4 | |
82 ================================ =========== ===== ==== | |
83 | |
84 This way you can easily filter for things like having a top prediction for | |
85 mitochondria (c2=='mito' and c4==1), or extracellular with a score of at | |
86 least 10 (c2=='extr' and 10<=c3), and so on. | |
87 | |
88 | |
89 **References** | |
90 | |
91 Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai, | |
92 WoLF PSORT: Protein Localization Predictor. | |
93 Nucleic Acids Research, 35(S2), W585-W587, doi:10.1093/nar/gkm259, 2007. | |
94 | |
95 Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai. | |
96 Protein Subcellular Localization Prediction with WoLF PSORT. | |
97 Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48, 2006. | |
98 | |
99 http://wolfpsort.org | |
100 | |
101 </help> | |
102 </tool> |