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annotate r_manova.xml @ 0:59bc96331073 draft default tip

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
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59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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1 <?xml version="1.0"?>
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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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
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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6 # it under the terms of the GNU General Public License as published by
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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7 # the Free Software Foundation, either version 3 of the License, or
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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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
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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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="3.1">
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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="3.1.0">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/14-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/20-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_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):
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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88 The data file containing beta diversity distance matrix.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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89 This file is the result of FROGS Phyloseq Beta Diversity tool.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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90
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91 .. class:: h3
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92
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93 Output
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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94
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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95 **html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): The review of Manova test.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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96
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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97 .. image:: static/images/frogs_images/phyloseq_manova.png
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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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**
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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102
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103 Contacts: frogs@inra.fr
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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104
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105 Repository: https://github.com/geraldinepascal/FROGS
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106 website: http://frogs.toulouse.inra.fr/
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107
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108 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
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109
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110 </help>
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111 <citations>
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112 <citation type="doi">10.1093/bioinformatics/btx791</citation>
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113 </citations>
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114
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115 </tool>