Mercurial > repos > peterjc > effectivet3
annotate tools/effectiveT3/effectiveT3.xml @ 23:69ab4d862db2 draft
v0.0.17 Used cached URL, python style updates
| author | peterjc |
|---|---|
| date | Wed, 01 Feb 2017 09:20:27 -0500 |
| parents | f5e52dd0935f |
| children | d6976a4c055b |
| rev | line source |
|---|---|
| 23 | 1 <tool id="effectiveT3" name="Effective T3" version="0.0.17"> |
| 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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6 <stdio> |
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7 <!-- Anything other than zero is an error --> |
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8 <exit_code range="1:" /> |
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9 <exit_code range=":-1" /> |
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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> | |
| 18 | 53 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> |
| 54 <param name="module" value="std_2_0_2" /> | |
| 55 <param name="type" value="cutoff" /> | |
| 20 | 56 <param name="cutoff" value="0.8" /> |
| 18 | 57 <output name="tabular_file" file="four_human_proteins.effectiveT3_std2.tabular" ftype="tabular" /> |
| 58 </test> | |
| 59 <test> | |
| 2 | 60 <param name="fasta_file" value="empty.fasta" ftype="fasta" /> |
| 61 <param name="module" value="plant" /> | |
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62 <param name="type" value="sensitive" /> |
| 2 | 63 <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" /> |
| 64 </test> | |
| 65 </tests> | |
| 66 <help> | |
| 67 | |
| 68 **What it does** | |
| 69 | |
| 70 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins. | |
| 71 | |
| 72 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein): | |
| 73 | |
| 74 ====== ============================================================================== | |
| 75 Column Description | |
| 76 ------ ------------------------------------------------------------------------------ | |
| 77 1 Sequence identifier | |
| 78 2 Sequence description (from the FASTA file) | |
| 79 3 Score (between 0 and 1, or negative for an error such as a very short peptide) | |
| 80 4 Predicted effector (true/false) | |
| 81 ====== ============================================================================== | |
| 82 | |
| 83 | |
| 84 **References** | |
| 85 | |
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86 If you use this Galaxy tool in work leading to a scientific publication please |
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87 cite the following papers: |
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88 |
| 13 | 89 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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90 Galaxy tools and workflows for sequence analysis with applications |
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91 in molecular plant pathology. PeerJ 1:e167 |
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92 http://dx.doi.org/10.7717/peerj.167 |
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93 |
| 13 | 94 Jehl, Arnold and Rattei (2011). |
| 2 | 95 Effective - a database of predicted secreted bacterial proteins |
| 13 | 96 Nucleic Acids Research, 39(Database issue), D591-5. |
| 2 | 97 http://dx.doi.org/10.1093/nar/gkq1154 |
| 98 | |
| 13 | 99 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei (2009). |
| 2 | 100 Sequence-based prediction of type III secreted proteins. |
| 13 | 101 PLoS Pathog. 5(4):e1000376. |
| 2 | 102 http://dx.doi.org/10.1371/journal.ppat.1000376 |
| 103 | |
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104 See also http://effectors.org/ |
| 2 | 105 |
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106 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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107 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 |
| 2 | 108 </help> |
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109 <citations> |
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110 <citation type="doi">10.7717/peerj.167</citation> |
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111 <citation type="doi">10.1093/nar/gkq1154</citation> |
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112 <citation type="doi">10.1371/journal.ppat.1000376</citation> |
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113 </citations> |
| 2 | 114 </tool> |