Mercurial > repos > frogs > frogs_2_0_0

annotate r_structure.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 Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="1.0.0">
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19 <description>with heatmap plot and ordination plot</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_structure.py
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28 --html $html
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29 --rdata $data
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30 --varExp $varExp
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31 --ordination-method $method
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32 --distance-matrix $distance
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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 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 <param name="distance" format="tabular" type="data" label="The beta diversity distance matrix file" help="These file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
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40 <validator type="empty_field" message="This parameter is required." />
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41 </param>
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42 <!-- Parameters -->
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43 <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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44 <validator type="empty_field" message="This parameter is required." />
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45 </param>
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46 <param name="method" type="select" label="Ordination method">
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47 <option value="MDS" >MDS/PCoA</option>
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48 <option value="NMDS" >NMDS</option>
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49 <option value="DPCoA" >DPCoA</option>
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50 </param>
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51 </inputs>
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52 <outputs>
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53 <data format="html" name="html" label="${tool.name}: structure.html" from_work_dir="structure.html"/>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="data" value="references/11-phylo_import.Rdata" />
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58 <param name="varExp" value="EnvType" />
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59 <param name="method" value="MDS" />
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60 <param name="distance" value="references/Unifrac.tsv" />
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61 <!--output name="html" file="references/15-phylo_structure.html" compare="sim_size" delta="10" /-->
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62 <output name="html">
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63 <assert_contents>
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64 <has_text_matching expression="html\sxmlns=.*" />
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65 <has_text_matching expression="application/json.*DesLardons" />
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66 </assert_contents>
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67 </output>
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68
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69 </test>
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70 </tests>
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71 <help>
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72
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73 .. image:: static/images/FROGS_logo.png
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74 :height: 144
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75 :width: 110
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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 What it does
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80
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81 Using `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ and customized R function, this tool constructs heatmap plot and ordination plot with the `ordination methods &lt;https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html#ordination-methods&gt;`_ to visualise data structure.
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82
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83 .. class:: infomark page-header h2
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84
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85 Inputs/Outputs
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86
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87 .. class:: h3
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88
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89 Input
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90
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91 **data file** (format rdata):
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92 The informations of data in one phyloseq object.
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93 This file is the result of "FROGS Phyloseq Import Data tool".
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94
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95 **distance file** (format tabular):
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96 The data file containing beta diversity distance matrix.
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97 This file is the result of "FROGS Phyloseq Beta Diversity tool".
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98
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99 .. class:: h3
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100
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101 Output
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102
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103 **html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
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104
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105 The review of data structure with an ordination plot and with an heatmap plot:
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106
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107 .. image:: static/images/phyloseq_plot_sample_ellipse.png
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108 :height: 343
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109 :width: 450
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110
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111 .. image:: static/images/phyloseq_plot_heatmap_red.png
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112 :height: 343
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113 :width: 450
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114
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115 .. class:: infomark page-header h2
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116
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117 **Contact**
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118
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119 Contacts: frogs@inra.fr
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120
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121 Repository: https://github.com/geraldinepascal/FROGS
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122
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123 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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124
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125 Depending on the help provided you can cite us in acknowledgements, references or both.
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126
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127 </help>
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128 <citations>
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129 <citation type="doi">10.7287/peerj.preprints.386v1</citation>
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130 </citations>
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131 </tool>