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annotate tree.xml @ 5:828d2003af85 draft

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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.3 commit fb1bb0bebef3a4f756718905088b2b50c93cb50e"
author oinizan
date Fri, 04 Jun 2021 11:09:35 +0000
parents ea386220db3c
children 192cac570229
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27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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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 -->
5
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18 <tool id="FROGS_Tree" name="FROGS Tree" version="3.2.3">
0
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19 <description>Reconstruction of phylogenetic tree </description>
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20 <requirements>
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21 <requirement type="package" version="3.2.3">frogs</requirement>
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22 <requirement type="package" version="7.407">mafft</requirement>
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23 <requirement type="package" version="2.1.09">fasttree</requirement>
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24 <requirement type="package" version="4.0.5">r-base</requirement>
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25 <requirement type="package" version="4.0">r-essentials</requirement>
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26 <requirement type="package" version="2.7.0">r-phangorn</requirement>
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27 </requirements>
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28 <stdio>
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29 <exit_code range="1:" />
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30 <exit_code range=":-1" />
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31 </stdio>
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32 <command>
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33 tree.py
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34 --input-sequences $input_otu
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35 --biom-file $biomfile
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36 --nb-cpus \${GALAXY_SLOTS:-1}
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37 --out-tree $out_tree
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38 --html $html
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39 </command>
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40 <inputs>
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41 <!-- Files -->
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42 <param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false">
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43 <validator type="empty_field" message="This parameter is required." />
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44 </param>
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45 <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false">
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46 <validator type="empty_field" message="This parameter is required." />
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47 </param>
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48 </inputs>
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49 <outputs>
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50 <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/>
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51 <data format="html" name="html" label="${tool.name}: report.html" from_work_dir="summary.html"/>
0
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="input_otu" value="references/09-normalisation.fasta"/>
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56 <param name="biomfile" value="references/09-normalisation.biom"/>
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57 <output name="out_tree" value="references/15-tree-mafft.nwk" compare="sim_size" delta="30"/>
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58 <output name="html" value="references/15-tree-mafft.html" compare="diff" lines_diff="2"/>
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59 <output name="html" value="references/15-tree-mafft.html" compare="sim_size" delta="30"/>
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60 <output name="html">
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61 <assert_contents>
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62 <has_text_matching expression="FROGS\sTree" />
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63 <has_text_matching expression="abundance_removed.*:\s0" />
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64 <has_text_matching expression="abundance_kept.*:\s300" />
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65 <has_text_matching expression="otu_removed.*:\s0" />
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66 <has_text_matching expression="otu_kept.*:\s52" />
0
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67 </assert_contents>
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68 </output>
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69 </test>
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70 </tests>
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71 <help>
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72 .. image:: static/images/FROGS_logo.png
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73 :height: 144
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74 :width: 110
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75
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76 .. class:: infomark page-header h2
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77
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78 What it does
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79
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80 Creation of a multiple alignment of OTUs with `Mafft &lt;http://mafft.cbrc.jp/alignment/software&gt;`_.
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81 And creation of a rooted phylogenetic tree with `FastTree &lt;http://www.microbesonline.org/fasttree/&gt;`_ and `Phangorn R package &lt;https://cran.r-project.org/web/packages/phangorn/index.html&gt;`_.
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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
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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87 .. class:: h3
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88
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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89 Input
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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90
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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91 **OTUs fasta file**:
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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92
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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93 The OTUs sequence file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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94 Careful: FROGS Tree works only with less than 10 000 sequences!
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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95
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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96 .. image:: static/images/FROGS_tree_otufile.png
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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97
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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98 **OTUs biom file**:
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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99
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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100 The OTUs biom file (format `biom1 &lt;http://biom-format.org/documentation/format_versions/biom-1.0.html&gt;`_).
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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101 This file can be obtained in particular with the FROGS pipeline.
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102
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103 .. class:: h3
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104
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105 Outputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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106
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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107 **Newick file** (tree.nwk):
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108
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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109 The phylogenetic tree in Newick format (format `nwk or nhx &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_).
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110
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111 .. image:: static/images/FROGS_nwk_treefile.png
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112
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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113 **Html file** (summary.html):
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114
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115 The summary file describing which OTUs are contained or not in the phylogenetic tree.
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116
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117 .. class:: infomark page-header h2
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118
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119 **Contact**
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120
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121 Contacts: frogs-support@inrae.fr
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122
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123 Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
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124
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125 Website: http://frogs.toulouse.inrae.fr/
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126
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127 Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. &lt;https://doi.org/10.1093/bioinformatics/btx791&gt;`_
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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128
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129 </help>
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130 </tool>