Mercurial > repos > peterjc > tmhmm_and_signalp
annotate tools/protein_analysis/wolf_psort.xml @ 23:e1996f0f4e85 draft default tip
"v0.2.13 - Python 3 fix for raising StopIteration"
author | peterjc |
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date | Thu, 17 Jun 2021 17:59:33 +0000 |
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23 | 1 <tool id="wolf_psort" name="WoLF PSORT" version="0.0.12"> |
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2 <description>Eukaryote protein subcellular localization prediction</description> |
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3 <requirements> |
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4 <requirement type="package">wolfpsort</requirement> |
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5 </requirements> |
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6 <version_command> |
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7 python $__tool_directory__/wolf_psort.py --version |
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8 </version_command> |
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9 <command detect_errors="aggressive"> |
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10 python $__tool_directory__/wolf_psort.py $organism "\$GALAXY_SLOTS" '$fasta_file' '$tabular_file' |
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11 </command> |
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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> |
14 | 23 <tests> |
24 <test> | |
25 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/> | |
26 <param name="organism" value="animal"/> | |
27 <output name="tabular_file" file="four_human_proteins.wolf_psort.tabular" ftype="tabular"/> | |
28 </test> | |
29 <test> | |
30 <param name="fasta_file" value="empty.fasta" ftype="fasta"/> | |
31 <param name="organism" value="animal"/> | |
32 <output name="tabular_file" file="empty_wolf_psort.tabular" ftype="tabular"/> | |
33 </test> | |
34 <test> | |
35 <param name="fasta_file" value="empty.fasta" ftype="fasta"/> | |
36 <param name="organism" value="plant"/> | |
37 <output name="tabular_file" file="empty_wolf_psort.tabular" ftype="tabular"/> | |
38 </test> | |
39 <test> | |
40 <param name="fasta_file" value="empty.fasta" ftype="fasta"/> | |
41 <param name="organism" value="fungi"/> | |
42 <output name="tabular_file" file="empty_wolf_psort.tabular" ftype="tabular"/> | |
43 </test> | |
44 </tests> | |
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45 <help> |
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46 |
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47 **What it does** |
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48 |
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49 This calls the WoLF PSORT tool for prediction of eukaryote protein subcellular localization. |
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50 |
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51 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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52 |
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53 ====== =================== |
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54 Column Description |
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55 ------ ------------------- |
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56 1 Sequence identifier |
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57 2 Compartment |
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58 3 Score |
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59 4 Prediction rank |
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60 ====== =================== |
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61 |
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62 |
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63 **Localization Compartments** |
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64 |
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65 The table below gives the WoLF PSORT localization site definitions, and the corresponding Gene Ontology (GO) term. |
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66 |
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67 ====== ===================== ===================== |
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68 Abbrev Localization Site GO Cellular Component |
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69 ------ --------------------- --------------------- |
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70 chlo chloroplast 0009507, 0009543 |
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71 cyto cytosol 0005829 |
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72 cysk cytoskeleton 0005856(2) |
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73 E.R. endoplasmic reticulum 0005783 |
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74 extr extracellular 0005576, 0005618 |
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75 golg Golgi apparatus 0005794(1) |
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76 lyso lysosome 0005764 |
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77 mito mitochondria 0005739 |
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78 nucl nuclear 0005634 |
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79 pero peroxisome 0005777(2) |
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80 plas plasma membrane 0005886 |
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81 vacu vacuolar membrane 0005774(2) |
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82 ====== ===================== ===================== |
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83 |
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84 Numbers in parentheses, such as "0005856(2)" indicate that descendant "part_of" |
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85 cellular components were also included, up to the specified depth (2 in this case). |
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86 For example, all of the children and grandchildren of "GO:0005856" were |
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87 included as "cysk". |
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88 |
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89 Additionally compound predictions like mito_nucl are also given. |
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90 |
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91 |
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92 **Notes** |
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93 |
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94 The raw output from WoLF PSORT looks like this (space separated), showing two proteins: |
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95 |
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96 ================================ ============================================ |
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97 gi|301087619|ref|XP_002894699.1| extr 12, mito 4, E.R. 3, golg 3, mito_nucl 3 |
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98 gi|301087623|ref|XP_002894700.1| extr 21, mito 2, cyto 2, cyto_mito 2 |
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99 ================================ ============================================ |
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100 |
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101 This is reformatted into a tabular file as follows for use in Galaxy: |
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102 |
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103 ================================ =========== ===== ==== |
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104 #ID Compartment Score Rank |
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105 -------------------------------- ----------- ----- ---- |
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106 gi|301087619|ref|XP_002894699.1| extr 12 1 |
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107 gi|301087619|ref|XP_002894699.1| mito 4 2 |
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108 gi|301087619|ref|XP_002894699.1| E.R. 3 3 |
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109 gi|301087619|ref|XP_002894699.1| golg 3 4 |
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110 gi|301087619|ref|XP_002894699.1| mito_nucl 3 5 |
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111 gi|301087623|ref|XP_002894700.1| extr 21 1 |
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112 gi|301087623|ref|XP_002894700.1| mito 2 2 |
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113 gi|301087623|ref|XP_002894700.1| cyto 2 3 |
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114 gi|301087623|ref|XP_002894700.1| cyto_mito 2 4 |
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115 ================================ =========== ===== ==== |
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116 |
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117 This way you can easily filter for things like having a top prediction for |
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118 mitochondria (c2=='mito' and c4==1), or extracellular with a score of at |
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119 least 10 (c2=='extr' and 10<=c3), and so on. |
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120 |
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121 |
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122 **References** |
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123 |
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124 If you use this Galaxy tool in work leading to a scientific publication please |
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125 cite the following papers: |
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126 |
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127 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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128 Galaxy tools and workflows for sequence analysis with applications |
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129 in molecular plant pathology. PeerJ 1:e167 |
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130 https://doi.org/10.7717/peerj.167 |
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131 |
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132 Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai (2007). |
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133 WoLF PSORT: Protein Localization Predictor. |
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134 Nucleic Acids Research, 35(S2), W585-W587. |
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135 https://doi.org/10.1093/nar/gkm259 |
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136 |
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137 Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai (2006). |
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138 Protein Subcellular Localization Prediction with WoLF PSORT. |
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139 Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48. |
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140 |
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141 See also http://wolfpsort.org |
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142 |
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143 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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144 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp |
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145 </help> |
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146 <citations> |
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147 <citation type="doi">10.7717/peerj.167</citation> |
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148 <citation type="doi">10.1093/nar/gkm259</citation> |
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149 </citations> |
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150 </tool> |