Mercurial > repos > peterjc > tmhmm_and_signalp
annotate tools/protein_analysis/wolf_psort.xml @ 9:e52220a9ddad draft
Uploaded v0.1.2
Use the new <stdio> settings in the XML wrappers to catch errors.
Obeys SGE style XNSLOTS environment variable for thread count (otherwise default to 4).
author | peterjc |
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date | Fri, 25 Jan 2013 06:08:31 -0500 |
parents | a290c6d4e658 |
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9 | 1 <tool id="wolf_psort" name="WoLF PSORT" version="0.0.2"> |
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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> |
9 | 7 <stdio> |
8 <!-- Anything other than zero is an error --> | |
9 <exit_code range="1:" /> | |
10 <exit_code range=":-1" /> | |
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 * Sequence identifier |
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35 * Compartment |
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36 * Score |
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37 * Prediction rank |
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38 |
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39 |
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40 **Localization Compartments** |
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41 |
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42 The table below gives the WoLF PSORT localization site definitions, and the corresponding Gene Ontology (GO) term. |
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43 |
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44 ====== ===================== ===================== |
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45 Abbrev Localization Site GO Cellular Component |
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46 ------ --------------------- --------------------- |
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47 chlo chloroplast 0009507, 0009543 |
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48 cyto cytosol 0005829 |
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49 cysk cytoskeleton 0005856(2) |
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50 E.R. endoplasmic reticulum 0005783 |
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51 extr extracellular 0005576, 0005618 |
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52 golg Golgi apparatus 0005794(1) |
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53 lyso lysosome 0005764 |
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54 mito mitochondria 0005739 |
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55 nucl nuclear 0005634 |
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56 pero peroxisome 0005777(2) |
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57 plas plasma membrane 0005886 |
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58 vacu vacuolar membrane 0005774(2) |
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59 ====== ===================== ===================== |
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60 |
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61 Additionally compound predictions like mito_nucl are also given. |
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62 |
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63 |
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64 **Notes** |
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65 |
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66 The raw output from WoLF PSORT looks like this (space separated), showing two proteins: |
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67 |
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68 ================================ ============================================ |
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69 gi|301087619|ref|XP_002894699.1| extr 12, mito 4, E.R. 3, golg 3, mito_nucl 3 |
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70 gi|301087623|ref|XP_002894700.1| extr 21, mito 2, cyto 2, cyto_mito 2 |
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71 ================================ ============================================ |
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72 |
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73 This is reformatted into a tabular file as follows for use in Galaxy: |
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74 |
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75 ================================ =========== ===== ==== |
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76 #ID Compartment Score Rank |
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77 -------------------------------- ----------- ----- ---- |
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78 gi|301087619|ref|XP_002894699.1| extr 12 1 |
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79 gi|301087619|ref|XP_002894699.1| mito 4 2 |
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80 gi|301087619|ref|XP_002894699.1| E.R. 3 3 |
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81 gi|301087619|ref|XP_002894699.1| golg 3 4 |
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82 gi|301087619|ref|XP_002894699.1| mito_nucl 3 5 |
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83 gi|301087623|ref|XP_002894700.1| extr 21 1 |
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84 gi|301087623|ref|XP_002894700.1| mito 2 2 |
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85 gi|301087623|ref|XP_002894700.1| cyto 2 3 |
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86 gi|301087623|ref|XP_002894700.1| cyto_mito 2 4 |
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87 ================================ =========== ===== ==== |
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88 |
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89 This way you can easily filter for things like having a top prediction for |
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90 mitochondria (c2=='mito' and c4==1), or extracellular with a score of at |
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91 least 10 (c2=='extr' and 10<=c3), and so on. |
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92 |
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93 |
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94 **References** |
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95 |
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96 Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai, |
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97 WoLF PSORT: Protein Localization Predictor. |
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98 Nucleic Acids Research, 35(S2), W585-W587, 2007. |
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99 http://dx.doi.org/10.1093/nar/gkm259 |
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100 |
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101 Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai. |
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102 Protein Subcellular Localization Prediction with WoLF PSORT. |
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103 Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48, 2006. |
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104 |
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105 http://wolfpsort.org |
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106 |
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107 </help> |
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108 </tool> |