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comparison sm_Tax4Fun.xml @ 0:4dcbac1c0acf draft

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Updated xml
author sarahinraauzeville
date Mon, 04 Dec 2017 09:25:11 -0500
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1 <!--# Copyright (C) 2014 INRA
2 # This program is free software: you can redistribute it and/or modify
3 # it under the terms of the GNU General Public License as published by
4 # the Free Software Foundation, either version 3 of the License, or
5 # (at your option) any later version.
6 #
7 # This program is distributed in the hope that it will be useful,
8 # but WITHOUT ANY WARRANTY; without even the implied warranty of
9 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
10 # GNU General Public License for more details.
11 #
12 # You should have received a copy of the GNU General Public License
13 # along with this program. If not, see http://www.gnu.org/licenses/.
14 #-->
15 <tool id="sm_Tax4Fun" name="Tax4Fun">
16 <description> predicts the functional or metabolic capabilities of microbial communities based on 16S data samples</description>
17 <command interpreter="perl">sm_Tax4Fun.pl
18 --input $input
19 --out $output
20 --reference $reference
21 </command>
22 <inputs>
23 <param format="csv, tabular" name="input" type="data" label="Input filelist containing the OTU table and sample (2 columns only)"/>
24 <param name="reference" type="select" label="Folder location of the unzipped reference data">
25 <option value="/galaxydata/galaxy-prod/my_tools/sm_Tax4Fun/SILVA123/">SILVA123</option>
26 <option value="No">OTHER TODO</option>
27 </param>
28 </inputs>
29 <outputs>
30 <data format="txt" name="output" label ="Tax4Fun result file"/>
31 </outputs>
32 <help>
33
34
35 .. class:: infomark
36
37 PLEASE READ THIS MANUAL TO USE TAX4FUN: http://genoweb.toulouse.inra.fr/~formation/GALAXY_news/howto3_Tax4Fun.pdf
38
39
40
41 .. class:: infomark
42
43
44 Package:Tax4Fun
45
46 Prediction of functional profiles from amplicon-data
47
48 Description:
49
50 Prediction of functional and metabolic profiles from amplicon-data using the Tax4Fun approach
51
52 Usage:
53
54 Tax4Fun(Tax4FunInput, folderReferenceData, fctProfiling = TRUE, refProfile = "UProC", shortReadMode = TRUE, normCopyNo = TRUE)
55
56 Arguments:
57
58 Tax4FunInput: (required): list containing the OTU table and sample names, e.g. imported with the functions ‘importQIIMEBiomData’, ‘importQIIMEData’, or ‘importSilvaNgsData’
59
60 folderReferenceData: (required): a character vector with one character string indicating the folder location of the unzipped reference data.
61
62
63 Details:
64
65 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.
66
67 Value:
68
69 A list containing the predicted functional or metabolic profiles and the FTU statistics
70
71 Pipeline:
72
73 This pipeline is used after FROGS pipeline.
74
75 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) »
76
77 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.
78
79 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).
80
81 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.
82
83 Warning: The only available reference is SILVA123.
84
85
86 Author(s) Tax4Fun:
87
88 Kathrin P. Asshauer email: kathrin@gobics.de
89
90 Author(s) Galaxy Wrapper Tax4Fun:
91
92 Sigenae Team.
93
94
95 References:
96
97 http://gobics.de/kathrin/Tax4Fun/Tax4Fun.html
98
99
100
101 ---
102
103 Version Galaxy Tool : V1.0.1
104
105 ---
106
107 Contacts : support.sigenae@inra.fr
108
109 E-learning available : http://genoweb.toulouse.inra.fr/~formation/GALAXY_news/howto3_Tax4Fun.pdf
110
111 Please cite :
112
113 Depending on the help provided you can cite us in acknowledgements, references or both.
114
115 Examples :
116 Acknowledgements
117 We wish to thank SIGENAE group and UMR-1280 PhAN Inra-Universite de Nantes.
118
119 References
120 X. SIGENAE [http://www.sigenae.org/]
121
122 </help>
123 </tool>