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annotate tools/effectiveT3/effectiveT3.xml @ 5:1ea715da1879 draft

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author peterjc
date Tue, 25 Nov 2014 08:28:24 -0500
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children 0f6eb4a75000
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1 <tool id="effectiveT3" name="Effective T3" version="0.0.13">
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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 <version_command interpreter="python">effectiveT3.py --version</version_command>
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7 <command interpreter="python">
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8 effectiveT3.py $module.fields.path
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9 #if $restrict.type=="cutoff":
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10 cutoff=$restrict.cutoff
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11 #else:
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12 $restrict.type
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13 #end if
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14 $fasta_file $tabular_file</command>
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15 <stdio>
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16 <!-- Anything other than zero is an error -->
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17 <exit_code range="1:" />
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18 <exit_code range=":-1" />
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19 </stdio>
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20 <inputs>
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21 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
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22 <param name="module" type="select" display="radio" label="Classification module">
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23 <options from_file="effectiveT3.loc">
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24 <column name="value" index="0"/>
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25 <column name="name" index="1"/>
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26 <column name="path" index="2"/>
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27 </options>
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28 </param>
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29 <conditional name="restrict">
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30 <param name="type" type="select" label="Cut-off setting">
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31 <option value="selective">Selective (threshold set in module)</option>
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32 <option value="sensitive">Sensitive (threshold set in module)</option>
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33 <option value="cutoff">User defined cut-off</option>
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34 </param>
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35 <when value="selective" />
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36 <when value="sensitive" />
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37 <when value="cutoff" >
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38 <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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39 </when>
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40 </conditional>
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41 </inputs>
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42 <outputs>
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43 <data name="tabular_file" format="tabular" label="Effective T3 $module.value_label on ${on_string}" />
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
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48 <param name="module" value="animal" />
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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"/>
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51 </test>
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52 <test>
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53 <param name="fasta_file" value="empty.fasta" ftype="fasta" />
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54 <param name="module" value="plant" />
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55 <param name="type" value="sensitive" />
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56 <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" />
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57 </test>
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58 </tests>
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59 <help>
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60
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61 **What it does**
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62
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63 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins.
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64
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65 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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66
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67 ====== ==============================================================================
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68 Column Description
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69 ------ ------------------------------------------------------------------------------
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70 1 Sequence identifier
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71 2 Sequence description (from the FASTA file)
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72 3 Score (between 0 and 1, or negative for an error such as a very short peptide)
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73 4 Predicted effector (true/false)
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74 ====== ==============================================================================
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75
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76
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77 **References**
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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
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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
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87 Jehl, Arnold and Rattei (2011).
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88 Effective - a database of predicted secreted bacterial proteins
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89 Nucleic Acids Research, 39(Database issue), D591-5.
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90 http://dx.doi.org/10.1093/nar/gkq1154
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91
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92 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei (2009).
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93 Sequence-based prediction of type III secreted proteins.
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94 PLoS Pathog. 5(4):e1000376.
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95 http://dx.doi.org/10.1371/journal.ppat.1000376
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96
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97 See also http://effectors.org/
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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
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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>
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107 </tool>