Mercurial > repos > frogs > frogs_2_0_0

annotate r_manova.xml @ 0:76c750c5f0d1 draft default tip

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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
author frogs
date Thu, 25 Oct 2018 05:01:13 -0400
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0
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1 <?xml version="1.0"?>
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2 <!--
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3 # Copyright (C) 2017 INRA
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4 #
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5 # This program is free software: you can redistribute it and/or modify
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6 # it under the terms of the GNU General Public License as published by
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7 # the Free Software Foundation, either version 3 of the License, or
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8 # (at your option) any later version.
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9 #
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10 # This program is distributed in the hope that it will be useful,
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 # GNU General Public License for more details.
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14 #
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15 # You should have received a copy of the GNU General Public License
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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17 -->
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18 <tool name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" version="1.0.0">
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19 <description>perform Multivariate Analysis of Variance (MANOVA)</description>
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20 <requirements>
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21 <requirement type="package" version="2.0.1">frogs</requirement>
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22 </requirements>
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23 <stdio>
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24 <exit_code range="1:" />
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25 <exit_code range=":-1" />
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26 </stdio>
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27 <command>r_manova.py
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28 --rdata $data
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29 --varExp "$varExp"
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30 --distance-matrix $method
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31 --html $html
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32 </command>
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33 <inputs>
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34 <!-- Files -->
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35 <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
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36 <validator type="empty_field" message="This parameter is required." />
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37 </param>
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38 <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
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39 <validator type="empty_field" message="This parameter is required." />
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40 </param>
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41 <!-- Parameters -->
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42 <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
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43 <validator type="empty_field" message="This parameter is required." />
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44 </param>
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45 </inputs>
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46 <outputs>
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47 <data format="html" name="html" label="${tool.name}: manova.html" from_work_dir="manova.html"/>
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="data" value="references/11-phylo_import.Rdata"/>
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52 <param name="varExp" value="EnvType"/>
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53 <param name="method" value="references/Unifrac.tsv"/>
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54 <!--output name="html" file="references/17-phylo_structure.html" compare="sim_size" delta="0" /-->
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55 <output name="html">
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56 <assert_contents>
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57 <has_text_matching expression="html\sxmlns=.*" />
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58 <has_text_matching expression="Phyloseq\s+\d+\.\d+\.\d+" />
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59 </assert_contents>
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60 </output>
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61 </test>
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62 </tests>
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63 <help>
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64
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65 .. image:: static/images/FROGS_logo.png
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66 :height: 144
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67 :width: 110
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68
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69 .. class:: infomark page-header h2
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70
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71 What it does
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72
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73 Using `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ and `vegan &lt;https://cran.r-project.org/web/packages/vegan/index.html&gt;`_ functions to perform Multivariate Analysis of Variance (MANOVA)
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74
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75 .. class:: infomark page-header h2
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76
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77 Inputs/Outputs
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78
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79 .. class:: h3
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80
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81 Input
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82
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83 **data file** (format RData):
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84 The informations of data in one phyloseq object.
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85 This is the result of FROGS Phyloseq Import Data tool.
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86
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87 **distance file** (format tabular):
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88 The data file containing beta diversity distance matrix.
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89 This file is the result of FROGS Phyloseq Beta Diversity tool.
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90
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91 .. class:: h3
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92
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93 Output
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94
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95 **html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): The review of Manova test.
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96
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97 .. image:: static/images/phyloseq_manova.png
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98
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99 .. class:: infomark page-header h2
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100
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101 **Contact**
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102
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103 Contacts: frogs@inra.fr
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104
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105 Repository: https://github.com/geraldinepascal/FROGS
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106
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107 Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
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108
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109 Depending on the help provided you can cite us in acknowledgements, references or both.
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110
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111 </help>
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112 <citations>
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113 <citation type="doi">10.7287/peerj.preprints.386v1</citation>
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114 </citations>
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115 </tool>