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annotate clusters_stat.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) 2015 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 id="FROGS_clusters_stat" name="FROGS Clusters stat" version="1.4.0">
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19 <description>Process some metrics on clusters.</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>
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28 clusters_stat.py
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29 --input-biom $biom
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30 --output-file $summary_file
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31 </command>
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32 <inputs>
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33 <param format="biom1" name="biom" type="data" label="Abundance file" help="Clusters abundance (format: BIOM)." optional="false" />
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34 </inputs>
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35 <outputs>
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36 <data format="html" name="summary_file" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="biom" value="references/04-affiliation.biom"/>
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41 <output name="summary_file" value="references/05-clustersStat.html" compare="sim_size" delta="0"/>
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42 </test>
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43 </tests>
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44 <help>
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45
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46 .. image:: static/images/FROGS_logo.png
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47 :height: 144
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48 :width: 110
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50
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51 .. class:: infomark page-header h2
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52
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53 What it does
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54
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55 FROGS Clusters stat computes several metrics and generates a HTML file describing clusters based on abundances, samples, ...
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56
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57
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58 .. class:: infomark page-header h2
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59
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60 Input/output
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61
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62 .. class:: h3
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63
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64 Input
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65
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66 **Abundance file**:
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67
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68 The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
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69
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70 The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format.
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71
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72 .. class:: h3
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74 Output
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76 **Summary file** (summary.html):
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78 Clusters metrics (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
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80 *Clusters distribution* : describes the sizes distribution of all clusters thank to boxplot and tables
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82 .. image:: static/images/FROGS_cluster_stat_clusterDistrib1.png
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83 :height: 426
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84 :width: 520
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86 .. image:: static/images/FROGS_cluster_stat_clusterDistrib2.png
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87 :height: 300
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88 :width: 460
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90 *Sequences distributions* : describes the sequences distribution among clusters
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92 .. image:: static/images/FROGS_cluster_stat_seq_dist.png
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93 :height: 326
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94 :width: 473
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95
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96 *Samples distribution* : describes clusters distribution among sample and give an `hierarchical clustering &lt;http://en.wikipedia.org/wiki/Hierarchical_clustering&gt;`_ on samples abundance profile (distance method = `braycurtis &lt;http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis&gt;`_, linkage method = average)
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97
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98 .. image:: static/images/FROGS_cluster_stat_sample_dist1.png
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99 :height: 400
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100 :width: 700
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101
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102 .. image:: static/images/FROGS_cluster_stat_sample_dist2.png
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103 :height: 350
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104 :width: 610
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105
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106 .. class:: infomark page-header h2
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107
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108 Advices
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109
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110 This is a very usefull tool to see the evolution of your OTU. Do not hesitate to run this tool after each FROGS step beginning at the clustering step.
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111
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112
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113 ----
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114
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115 **Contact**
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116
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117 Contacts: frogs@inra.fr
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118
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119 Repository: https://github.com/geraldinepascal/FROGS
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120
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121 Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
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122
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123 Depending on the help provided you can cite us in acknowledgements, references or both.
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124 </help>
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125 <citations>
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126 <citation type="doi">10.7287/peerj.preprints.386v1</citation>
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127 </citations>
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128 </tool>