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1 <!--# Copyright (C) 2014 INRA
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2 # This program is free software: you can redistribute it and/or modify
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3 # it under the terms of the GNU General Public License as published by
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4 # the Free Software Foundation, either version 3 of the License, or
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5 # (at your option) any later version.
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6 #
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7 # This program is distributed in the hope that it will be useful,
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8 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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9 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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10 # GNU General Public License for more details.
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11 #
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12 # You should have received a copy of the GNU General Public License
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13 # along with this program. If not, see http://www.gnu.org/licenses/.
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14 #-->
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15 <tool id="sm_Tax4Fun" name="Tax4Fun">
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16 <description> predicts the functional or metabolic capabilities of microbial communities based on 16S data samples</description>
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17 <command interpreter="perl">sm_Tax4Fun.pl
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18 --input $input
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19 --out $output
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20 --reference $reference
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21 </command>
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22 <inputs>
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23 <param format="csv, tabular" name="input" type="data" label="Input filelist containing the OTU table and sample. WARNING : 2 columns only with abundance on the left side and taxonomy on the right side."/>
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24 <param name="reference" type="select" label="Folder location of the unzipped reference data">
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25 <option value="/galaxydata/galaxy-prod/my_tools/sm_Tax4Fun/SILVA123/">SILVA123</option>
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26 <option value="No">OTHER TODO</option>
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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data format="txt" name="output" label ="Tax4Fun result file"/>
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31 </outputs>
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32 <help>
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33
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34
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35 .. class:: infomark
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36
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37 PLEASE READ THIS MANUAL TO USE TAX4FUN: http://genoweb.toulouse.inra.fr/~formation/GALAXY_news/howto3_Tax4Fun.pdf
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38
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39 .. image:: ${static_path}/images/tax4fun_wf.png
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40
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41
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42 Complete ready-to-use workflow available here : http://genoweb.toulouse.inra.fr/~formation/GALAXY_news/Galaxy-Workflow-Workflow_constructed_from_history__TAX4FUN_.ga
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43
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44 Pipeline:
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45
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46
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47 This pipeline is used after FROGS pipeline.
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48
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49 A- First, convert BIOM file result of FROGS in standard BIOM thanks to the following Galaxy tool : « FROGS BIOM to std BIOM Converts a FROGS BIOM in fully compatible BIOM. (Galaxy Version 1.1.0) »
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50
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51 B- Then convert standard BIOM file in TSV file with « FROGS BIOM to TSV Converts a BIOM file in TSV file. (Galaxy Version 2.1.0) » tool.
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52
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53 C- Select only 2 columns: abundance totale and taxonomy. To recover these data from the previous dataset, you can use « Cut columns from a table (Galaxy Version 1.0.2) » to generate 2 files: one file with Taxonomy and another with abundance_sum. The tool « Paste two files side by side (Galaxy Version 1.0.0) » paste these 2 files in one (first column: abundance, second column: taxonomy).
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54
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55 .. image:: ${static_path}/images/tax4fun_inputfile.png
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56
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57 E- Then « Tax4Fun predicts the functional or metabolic capabilities of microbial communities based on 16S data samples (Galaxy Version 1.0.0) » sort data, rewrite taxonomy, sum abundance for the same taxonomy.
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58
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59 Warning: The only available reference is SILVA123.
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60
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61
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62 .. class:: infomark
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63
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64
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65 Package Tax4Fun : Prediction of functional profiles from amplicon-data
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66
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67
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68 Description:
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69
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70 Prediction of functional and metabolic profiles from amplicon-data using the Tax4Fun approach
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71
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72 Usage:
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73
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74 Tax4Fun(Tax4FunInput, folderReferenceData, fctProfiling = TRUE, refProfile = "UProC", shortReadMode = TRUE, normCopyNo = TRUE)
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75
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76 Arguments:
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77
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78 Tax4FunInput: (required): list containing the OTU table and sample names, e.g. imported with the functions ‘importQIIMEBiomData’, ‘importQIIMEData’, or ‘importSilvaNgsData’ folderReferenceData: (required): a character vector with one character string indicating the folder location of the unzipped reference data.
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79
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80
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81 Details:
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82
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83 Tax4Fun predicts the functional and metabolic capabilities of microbial communities based on 16S data samples. Tax4Fun provides a good functional approximation to functional profiles obtained through metagenome sequencing. Tax4Fun can be used as a first instance functional profiling tool for an estimate of the functional capabilities of microbial communities based on amplicon data. Tax4Fun is applicable to output as obtained through the SILVAngs web server or the application of QIIME against the SILVA database.
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84
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85 Value:
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86
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87 A list containing the predicted functional or metabolic profiles and the FTU statistics
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88
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89
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90 Author(s) Tax4Fun:
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91
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92 Kathrin P. Asshauer email: kathrin@gobics.de
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93
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94 Author(s) Galaxy Wrapper Tax4Fun:
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95
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96 Sigenae Team.
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97
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98
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99 References:
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100
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101 http://gobics.de/kathrin/Tax4Fun/Tax4Fun.html
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102
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103
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104
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105 ---
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106
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107 Version Galaxy Tool : V1.0.1
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108
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109 ---
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110
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111 Contacts : support.sigenae@inra.fr
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112
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113 E-learning available : http://genoweb.toulouse.inra.fr/~formation/GALAXY_news/howto3_Tax4Fun.pdf
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114
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115 Please cite :
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116
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117 Depending on the help provided you can cite us in acknowledgements, references or both.
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118
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119 Example of acknowledgements: We wish to thank SIGENAE group and UMR-1280 PhAN Inra-Universite de Nantes.
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120
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121 Example of references : X. SIGENAE [http://www.sigenae.org/]
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122
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123 </help>
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124 </tool>
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