Mercurial > repos > peterjc > effectivet3
annotate tools/effectiveT3/effectiveT3.xml @ 17:c9ef96985153 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/effectiveT3 commit 3c6f0dca0e1318eecd1e07d177ffc5752b4f6c95
| author | peterjc |
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| date | Thu, 21 May 2015 10:48:40 -0400 |
| parents | bc93121586ba |
| children | 999776f0aee4 |
| rev | line source |
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bc93121586ba
planemo upload for https://github.com/peterjc/pico_galaxy/tools/effectiveT3/d3dbd53ff1ef0e33071da5665d1a9ed099230a6f
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1 <tool id="effectiveT3" name="Effective T3" version="0.0.15"> |
| 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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bc93121586ba
planemo upload for https://github.com/peterjc/pico_galaxy/tools/effectiveT3/d3dbd53ff1ef0e33071da5665d1a9ed099230a6f
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6 <stdio> |
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bc93121586ba
planemo upload for https://github.com/peterjc/pico_galaxy/tools/effectiveT3/d3dbd53ff1ef0e33071da5665d1a9ed099230a6f
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7 <!-- Anything other than zero is an error --> |
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bc93121586ba
planemo upload for https://github.com/peterjc/pico_galaxy/tools/effectiveT3/d3dbd53ff1ef0e33071da5665d1a9ed099230a6f
peterjc
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8 <exit_code range="1:" /> |
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bc93121586ba
planemo upload for https://github.com/peterjc/pico_galaxy/tools/effectiveT3/d3dbd53ff1ef0e33071da5665d1a9ed099230a6f
peterjc
parents:
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9 <exit_code range=":-1" /> |
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bc93121586ba
planemo upload for https://github.com/peterjc/pico_galaxy/tools/effectiveT3/d3dbd53ff1ef0e33071da5665d1a9ed099230a6f
peterjc
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10 </stdio> |
| 2 | 11 <version_command interpreter="python">effectiveT3.py --version</version_command> |
| 12 <command interpreter="python"> | |
| 13 effectiveT3.py $module.fields.path | |
| 14 #if $restrict.type=="cutoff": | |
| 15 cutoff=$restrict.cutoff | |
| 16 #else: | |
| 17 $restrict.type | |
| 18 #end if | |
| 19 $fasta_file $tabular_file</command> | |
| 20 <inputs> | |
| 21 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> | |
| 22 <param name="module" type="select" display="radio" label="Classification module"> | |
| 23 <options from_file="effectiveT3.loc"> | |
| 24 <column name="value" index="0"/> | |
| 25 <column name="name" index="1"/> | |
| 26 <column name="path" index="2"/> | |
| 27 </options> | |
| 28 </param> | |
| 29 <conditional name="restrict"> | |
| 30 <param name="type" type="select" label="Cut-off setting"> | |
| 31 <option value="selective">Selective (threshold set in module)</option> | |
| 32 <option value="sensitive">Sensitive (threshold set in module)</option> | |
| 33 <option value="cutoff">User defined cut-off</option> | |
| 34 </param> | |
| 35 <when value="selective" /> | |
| 36 <when value="sensitive" /> | |
| 37 <when value="cutoff" > | |
| 38 <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1" /> | |
| 39 </when> | |
| 40 </conditional> | |
| 41 </inputs> | |
| 42 <outputs> | |
| 11 | 43 <data name="tabular_file" format="tabular" label="Effective T3 $module.value_label on ${on_string}" /> |
| 2 | 44 </outputs> |
| 45 <tests> | |
| 46 <test> | |
| 47 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> | |
| 48 <param name="module" value="animal" /> | |
| 49 <param name="type" value="selective" /> | |
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50 <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" lines_diff="2"/> |
| 2 | 51 </test> |
| 52 <test> | |
| 53 <param name="fasta_file" value="empty.fasta" ftype="fasta" /> | |
| 54 <param name="module" value="plant" /> | |
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55 <param name="type" value="sensitive" /> |
| 2 | 56 <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" /> |
| 57 </test> | |
| 58 </tests> | |
| 59 <help> | |
| 60 | |
| 61 **What it does** | |
| 62 | |
| 63 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins. | |
| 64 | |
| 65 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein): | |
| 66 | |
| 67 ====== ============================================================================== | |
| 68 Column Description | |
| 69 ------ ------------------------------------------------------------------------------ | |
| 70 1 Sequence identifier | |
| 71 2 Sequence description (from the FASTA file) | |
| 72 3 Score (between 0 and 1, or negative for an error such as a very short peptide) | |
| 73 4 Predicted effector (true/false) | |
| 74 ====== ============================================================================== | |
| 75 | |
| 76 | |
| 77 **References** | |
| 78 | |
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79 If you use this Galaxy tool in work leading to a scientific publication please |
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80 cite the following papers: |
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81 |
| 13 | 82 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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83 Galaxy tools and workflows for sequence analysis with applications |
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84 in molecular plant pathology. PeerJ 1:e167 |
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85 http://dx.doi.org/10.7717/peerj.167 |
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86 |
| 13 | 87 Jehl, Arnold and Rattei (2011). |
| 2 | 88 Effective - a database of predicted secreted bacterial proteins |
| 13 | 89 Nucleic Acids Research, 39(Database issue), D591-5. |
| 2 | 90 http://dx.doi.org/10.1093/nar/gkq1154 |
| 91 | |
| 13 | 92 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei (2009). |
| 2 | 93 Sequence-based prediction of type III secreted proteins. |
| 13 | 94 PLoS Pathog. 5(4):e1000376. |
| 2 | 95 http://dx.doi.org/10.1371/journal.ppat.1000376 |
| 96 | |
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97 See also http://effectors.org/ |
| 2 | 98 |
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99 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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100 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 |
| 2 | 101 </help> |
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102 <citations> |
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103 <citation type="doi">10.7717/peerj.167</citation> |
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104 <citation type="doi">10.1093/nar/gkq1154</citation> |
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105 <citation type="doi">10.1371/journal.ppat.1000376</citation> |
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106 </citations> |
| 2 | 107 </tool> |