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annotate tools/protein_analysis/wolf_psort.xml @ 11:99b82a2b1272 draft

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Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
author peterjc
date Wed, 03 Apr 2013 10:49:10 -0400
parents e52220a9ddad
children 6365217cd3de
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11
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1 <tool id="wolf_psort" name="WoLF PSORT" version="0.0.3">
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2 <description>Eukaryote protein subcellular localization prediction</description>
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3 <command interpreter="python">
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4 wolf_psort.py $organism 8 $fasta_file $tabular_file
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5 ##I want the number of threads to be a Galaxy config option...
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6 </command>
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7 <stdio>
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8 <!-- Anything other than zero is an error -->
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9 <exit_code range="1:" />
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10 <exit_code range=":-1" />
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11 </stdio>
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12 <inputs>
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13 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
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14 <param name="organism" type="select" display="radio" label="Organism">
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15 <option value="animal">Animal</option>
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16 <option value="plant">Plant</option>
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17 <option value="fungi">Fungi</option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data name="tabular_file" format="tabular" label="WoLF PSORT $organism results" />
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22 </outputs>
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23 <requirements>
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24 <requirement type="binary">runWolfPsortSummary</requirement>
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25 </requirements>
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26 <help>
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27
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28 **What it does**
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29
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30 This calls the WoLF PSORT tool for prediction of eukaryote protein subcellular localization.
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31
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32 The input is a FASTA file of protein sequences, and the output is tabular with four columns (multiple rows per protein):
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33
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34 ====== ===================
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35 Column Description
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36 ------ -------------------
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37 1 Sequence identifier
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38 2 Compartment
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39 3 Score
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40 4 Prediction rank
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41 ====== ===================
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42
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43
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44 **Localization Compartments**
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45
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46 The table below gives the WoLF PSORT localization site definitions, and the corresponding Gene Ontology (GO) term.
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47
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48 ====== ===================== =====================
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49 Abbrev Localization Site GO Cellular Component
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50 ------ --------------------- ---------------------
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51 chlo chloroplast 0009507, 0009543
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52 cyto cytosol 0005829
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53 cysk cytoskeleton 0005856(2)
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54 E.R. endoplasmic reticulum 0005783
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55 extr extracellular 0005576, 0005618
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56 golg Golgi apparatus 0005794(1)
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57 lyso lysosome 0005764
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58 mito mitochondria 0005739
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59 nucl nuclear 0005634
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60 pero peroxisome 0005777(2)
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61 plas plasma membrane 0005886
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62 vacu vacuolar membrane 0005774(2)
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63 ====== ===================== =====================
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64
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65 Additionally compound predictions like mito_nucl are also given.
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66
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67
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68 **Notes**
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69
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70 The raw output from WoLF PSORT looks like this (space separated), showing two proteins:
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72 ================================ ============================================
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73 gi|301087619|ref|XP_002894699.1| extr 12, mito 4, E.R. 3, golg 3, mito_nucl 3
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74 gi|301087623|ref|XP_002894700.1| extr 21, mito 2, cyto 2, cyto_mito 2
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75 ================================ ============================================
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76
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77 This is reformatted into a tabular file as follows for use in Galaxy:
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78
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79 ================================ =========== ===== ====
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80 #ID Compartment Score Rank
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81 -------------------------------- ----------- ----- ----
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82 gi|301087619|ref|XP_002894699.1| extr 12 1
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83 gi|301087619|ref|XP_002894699.1| mito 4 2
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84 gi|301087619|ref|XP_002894699.1| E.R. 3 3
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85 gi|301087619|ref|XP_002894699.1| golg 3 4
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86 gi|301087619|ref|XP_002894699.1| mito_nucl 3 5
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87 gi|301087623|ref|XP_002894700.1| extr 21 1
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88 gi|301087623|ref|XP_002894700.1| mito 2 2
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89 gi|301087623|ref|XP_002894700.1| cyto 2 3
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90 gi|301087623|ref|XP_002894700.1| cyto_mito 2 4
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91 ================================ =========== ===== ====
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92
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93 This way you can easily filter for things like having a top prediction for
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94 mitochondria (c2=='mito' and c4==1), or extracellular with a score of at
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95 least 10 (c2=='extr' and 10&lt;=c3), and so on.
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96
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97
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98 **References**
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99
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100 Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai,
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101 WoLF PSORT: Protein Localization Predictor.
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102 Nucleic Acids Research, 35(S2), W585-W587, 2007.
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103 http://dx.doi.org/10.1093/nar/gkm259
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104
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105 Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai.
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106 Protein Subcellular Localization Prediction with WoLF PSORT.
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107 Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48, 2006.
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108
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109 http://wolfpsort.org
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110
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111 </help>
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112 </tool>