Mercurial > repos > peterjc > effectivet3
annotate tools/effectiveT3/effectiveT3.xml @ 35:e2711662802b draft default tip
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit d67596914a7bbe183851437eaafe8c7305877e5a-dirty
| author | peterjc |
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| date | Fri, 22 Feb 2019 10:13:22 -0500 |
| parents | 011cfce866f1 |
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| rev | line source |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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1 <tool id="effectiveT3" name="Effective T3" version="0.0.20"> |
| 2 | 2 <description>Find bacterial effectors in protein sequences</description> |
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3 <requirements> |
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4 <requirement type="package" version="1.0.1">effectiveT3</requirement> |
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5 </requirements> |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
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6 <version_command> |
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7 python $__tool_directory__/effectiveT3.py --version |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
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8 </version_command> |
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d6976a4c055b
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
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9 <command detect_errors="aggressive"> |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
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10 python $__tool_directory__/effectiveT3.py '$module.fields.path' |
| 2 | 11 #if $restrict.type=="cutoff": |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
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12 'cutoff=$restrict.cutoff' |
| 2 | 13 #else: |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
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14 '$restrict.type' |
| 2 | 15 #end if |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
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16 '$fasta_file' '$tabular_file' |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
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17 </command> |
| 2 | 18 <inputs> |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit e2fa1c599b6670b418479447fe5a181a97a6c834-dirty
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19 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> |
| 2 | 20 <param name="module" type="select" display="radio" label="Classification module"> |
| 21 <options from_file="effectiveT3.loc"> | |
| 22 <column name="value" index="0"/> | |
| 23 <column name="name" index="1"/> | |
| 24 <column name="path" index="2"/> | |
| 25 </options> | |
| 26 </param> | |
| 27 <conditional name="restrict"> | |
| 28 <param name="type" type="select" label="Cut-off setting"> | |
| 29 <option value="selective">Selective (threshold set in module)</option> | |
| 30 <option value="sensitive">Sensitive (threshold set in module)</option> | |
| 31 <option value="cutoff">User defined cut-off</option> | |
| 32 </param> | |
| 33 <when value="selective" /> | |
| 34 <when value="sensitive" /> | |
| 35 <when value="cutoff" > | |
| 36 <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1" /> | |
| 37 </when> | |
| 38 </conditional> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 11 | 41 <data name="tabular_file" format="tabular" label="Effective T3 $module.value_label on ${on_string}" /> |
| 2 | 42 </outputs> |
| 43 <tests> | |
| 44 <test> | |
| 45 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> | |
| 46 <param name="module" value="animal" /> | |
| 47 <param name="type" value="selective" /> | |
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48 <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" lines_diff="2"/> |
| 2 | 49 </test> |
| 50 <test> | |
| 18 | 51 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> |
| 52 <param name="module" value="std_2_0_2" /> | |
| 53 <param name="type" value="cutoff" /> | |
| 20 | 54 <param name="cutoff" value="0.8" /> |
| 18 | 55 <output name="tabular_file" file="four_human_proteins.effectiveT3_std2.tabular" ftype="tabular" /> |
| 56 </test> | |
| 57 <test> | |
| 2 | 58 <param name="fasta_file" value="empty.fasta" ftype="fasta" /> |
| 59 <param name="module" value="plant" /> | |
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60 <param name="type" value="sensitive" /> |
| 2 | 61 <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" /> |
| 62 </test> | |
| 63 </tests> | |
| 64 <help> | |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit e2fa1c599b6670b418479447fe5a181a97a6c834-dirty
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65 |
| 2 | 66 **What it does** |
| 67 | |
| 68 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins. | |
| 69 | |
| 70 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein): | |
| 71 | |
| 72 ====== ============================================================================== | |
| 73 Column Description | |
| 74 ------ ------------------------------------------------------------------------------ | |
| 75 1 Sequence identifier | |
| 76 2 Sequence description (from the FASTA file) | |
| 77 3 Score (between 0 and 1, or negative for an error such as a very short peptide) | |
| 78 4 Predicted effector (true/false) | |
| 79 ====== ============================================================================== | |
| 80 | |
| 81 | |
| 82 **References** | |
| 83 | |
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84 If you use this Galaxy tool in work leading to a scientific publication please |
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85 cite the following papers: |
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86 |
| 13 | 87 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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88 Galaxy tools and workflows for sequence analysis with applications |
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89 in molecular plant pathology. PeerJ 1:e167 |
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90 https://doi.org/10.7717/peerj.167 |
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91 |
| 13 | 92 Jehl, Arnold and Rattei (2011). |
| 2 | 93 Effective - a database of predicted secreted bacterial proteins |
| 13 | 94 Nucleic Acids Research, 39(Database issue), D591-5. |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty
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95 https://doi.org/10.1093/nar/gkq1154 |
| 2 | 96 |
| 13 | 97 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei (2009). |
| 2 | 98 Sequence-based prediction of type III secreted proteins. |
| 13 | 99 PLoS Pathog. 5(4):e1000376. |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty
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100 https://doi.org/10.1371/journal.ppat.1000376 |
| 2 | 101 |
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102 See also http://effectors.org/ |
| 2 | 103 |
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104 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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105 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 |
| 2 | 106 </help> |
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107 <citations> |
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108 <citation type="doi">10.7717/peerj.167</citation> |
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109 <citation type="doi">10.1093/nar/gkq1154</citation> |
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110 <citation type="doi">10.1371/journal.ppat.1000376</citation> |
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111 </citations> |
| 2 | 112 </tool> |