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

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author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
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1 <?xml version="1.0" encoding="UTF-8"?>
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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 Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="3.1">
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19 <description>with richness plot</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_alpha_diversity.py
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28 --rdata $data
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29 --varExp $varExp
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30 --alpha-measures $measures
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31 --alpha-out $alphaD
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32 --html $html
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33 </command>
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34 <inputs>
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35 <!-- Files -->
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36 <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This file is the result of FROGS Phyloseq Import Data tool." optional="false">
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37 <validator type="empty_field" message="This parameter is required." />
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38 </param>
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39 <!-- Parameters -->
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40 <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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41 <validator type="empty_field" message="This parameter is required." />
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42 </param>
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43 <param name="measures" type="select" label="The alpha diversity indices to compute" multiple="true" display="checkboxes">
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44 <option value="Observed" selected="True">Observed</option>
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45 <option value="Chao1" selected="True">Chao1</option>
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46 <option value="Shannon" selected="True">Shannon</option>
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47 <option value="InvSimpson" selected="True">InvSimpson</option>
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48 <option value="Simpson">Simpson</option>
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49 <option value="ACE">ACE</option>
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50 <option value="Fisher">Fisher</option>
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51 </param>
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52 </inputs>
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53 <outputs>
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54 <data format="tabular" name="alphaD" label="${tool.name}: alpha_diversity.tsv" from_work_dir="alpha_diversity.tsv"/>
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55 <data format="html" name="html" label="${tool.name}: alpha_diversity.html" from_work_dir="alpha_diversity.html"/>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="data" value="references/14-phylo_import.Rdata" />
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60 <param name="varExp" value="EnvType" />
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61 <param name="measures" value="Observed,Chao1,Shannon" />
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62 <output name="alphaD" file="references/16-phylo_alpha_div.tsv" compare="diff" lines_diff="0" />
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63 </test>
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64 </tests>
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65 <help>
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66
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67 .. image:: static/images/frogs_images/FROGS_logo.png
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68 :height: 144
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69 :width: 110
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70
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71 .. class:: infomark page-header h2
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72
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73 What it does
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74
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75 Using `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ and customized R function, this tool constructs richness plots to visualise sample alpha diversity.
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76
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77 .. class:: infomark page-header h2
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78
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79 Inputs/Outputs
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80
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81 .. class:: h3
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82
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83 Input
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84
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85 **Data file** (format RData):
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86 One phyloseq object containing OTU abundance table, their taxonomies (and optionnaly a phylogenetics tree, and the sample experiment metadata.
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87 This file is the result of "FROGS Phyloseq Import Data tool".
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88
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89 .. class:: h3
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90
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91 Output
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92
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93 **Html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): the review of richness plots and rarefaction curves.
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94
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95 .. image:: static/images/frogs_images/phyloseq_plot_richness.png
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96 :height: 400
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97 :width: 525
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98
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99 .. image:: static/images/frogs_images/phyloseq_plot_richness_box.png
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100 :height: 400
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101 :width: 499
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102
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103 .. image:: static/images/frogs_images/phyloseq_rarefaction_curves.png
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104 :height: 400
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105 :width: 498
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106
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107 **Alpha diversity table** (alpha_diversity.tsv):
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108 The data file containing table of alpha diversity indices.
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109
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110 .. image:: static/images/frogs_images/phyloseq_alpha_diversity_table.png
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111
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112 .. class:: infomark page-header h2
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113
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114 **Contact**
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115
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116 Contacts: frogs@inra.fr
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117
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118 Repository: https://github.com/geraldinepascal/FROGS
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119 website: http://frogs.toulouse.inra.fr/
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120
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121 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
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122
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123 </help>
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124 <citations>
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125 <citation type="doi">10.1093/bioinformatics/btx791</citation>
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126 </citations>
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127 </tool>