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1 <tool id="effectiveT3" name="Effective T3" version="0.0.11">
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2 <description>Find bacterial effectors in protein sequences</description>
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3 <version_command interpreter="python">effectiveT3.py --version</version_command>
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4 <command interpreter="python">
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5 effectiveT3.py $module.fields.path
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6 #if $restrict.type=="cutoff":
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7 cutoff=$restrict.cutoff
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8 #else:
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9 $restrict.type
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10 #end if
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11 $fasta_file $tabular_file</command>
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12 <stdio>
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13 <!-- Anything other than zero is an error -->
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14 <exit_code range="1:" />
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15 <exit_code range=":-1" />
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16 </stdio>
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17 <inputs>
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18 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
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19 <param name="module" type="select" display="radio" label="Classification module">
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20 <options from_file="effectiveT3.loc">
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21 <column name="value" index="0"/>
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22 <column name="name" index="1"/>
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23 <column name="path" index="2"/>
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24 </options>
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25 </param>
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26 <conditional name="restrict">
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27 <param name="type" type="select" label="Cut-off setting">
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28 <option value="selective">Selective (threshold set in module)</option>
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29 <option value="sensitive">Sensitive (threshold set in module)</option>
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30 <option value="cutoff">User defined cut-off</option>
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31 </param>
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32 <when value="selective" />
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33 <when value="sensitive" />
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34 <when value="cutoff" >
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35 <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1" />
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36 </when>
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37 </conditional>
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38 </inputs>
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39 <outputs>
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40 <data name="tabular_file" format="tabular" label="$module.value_label results" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
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45 <param name="module" value="animal" />
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46 <param name="type" value="selective" />
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47 <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" />
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48 </test>
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49 <test>
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50 <param name="fasta_file" value="empty.fasta" ftype="fasta" />
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51 <param name="module" value="plant" />
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52 <param name="type" value="sensistive" />
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53 <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" />
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54 </test>
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55 </tests>
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56 <help>
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57
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58 **What it does**
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59
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60 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins.
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61
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62 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein):
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63
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64 ====== ==============================================================================
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65 Column Description
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66 ------ ------------------------------------------------------------------------------
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67 1 Sequence identifier
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68 2 Sequence description (from the FASTA file)
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69 3 Score (between 0 and 1, or negative for an error such as a very short peptide)
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70 4 Predicted effector (true/false)
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71 ====== ==============================================================================
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72
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73
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74 **References**
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75
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76 Jehl, Arnold and Rattei.
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77 Effective - a database of predicted secreted bacterial proteins
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78 Nucleic Acids Research, 39(Database issue), D591-5, 2011.
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79 http://dx.doi.org/10.1093/nar/gkq1154
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80
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81 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
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82 Sequence-based prediction of type III secreted proteins.
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83 PLoS Pathog. 5(4):e1000376, 2009.
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84 http://dx.doi.org/10.1371/journal.ppat.1000376
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85
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86 http://effectors.org/
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87
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88 </help>
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89 </tool>
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