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annotate tree.xml @ 7:76dcbe930b1d draft

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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
author oinizan
date Wed, 18 Aug 2021 15:43:00 +0000
parents 192cac570229
children 7bf54edaba24
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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 -->
7
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18 <tool id="FROGS_Tree" name="FROGS Tree" version="@TOOL_VERSION@+galaxy2">
0
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19 <description>Reconstruction of phylogenetic tree </description>
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21 <macros>
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22 <import>macros.xml</import>
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23 </macros>
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24
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25 <expand macro="requirements" >
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26 <requirement type="package" version="7.407">mafft</requirement>
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27 <requirement type="package" version="2.1.9">fasttree</requirement>
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28 <requirement type="package" version="4.0">r-essentials</requirement>
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29 <requirement type="package" version="2.7.0">r-phangorn</requirement>
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30 </expand>
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31
0
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32 <stdio>
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33 <exit_code range="1:" />
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34 <exit_code range=":-1" />
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35 </stdio>
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36 <command>
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37 tree.py
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38 --input-sequences '$input_otu'
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39 --biom-file '$biomfile'
0
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40 --nb-cpus \${GALAXY_SLOTS:-1}
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41 --out-tree '$out_tree'
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42 --html '$html'
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43 </command>
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44 <inputs>
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45 <!-- Files -->
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46 <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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47 <validator type="empty_field" message="This parameter is required." />
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48 </param>
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49 <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false">
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50 <validator type="empty_field" message="This parameter is required." />
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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="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/>
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55 <data format="html" name="html" label="${tool.name}: report.html" from_work_dir="summary.html"/>
0
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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="input_otu" value="references/09-normalisation.fasta"/>
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60 <param name="biomfile" value="references/09-normalisation.biom"/>
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61 <output name="out_tree" value="references/15-tree-mafft.nwk" compare="sim_size" delta="30"/>
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62 <output name="html" value="references/15-tree-mafft.html" compare="diff" lines_diff="2"/>
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63 <output name="html" value="references/15-tree-mafft.html" compare="sim_size" delta="30"/>
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64 <output name="html">
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65 <assert_contents>
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66 <has_text_matching expression="FROGS\sTree" />
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67 <has_text_matching expression="abundance_removed.*:\s0" />
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68 <has_text_matching expression="abundance_kept.*:\s300" />
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69 <has_text_matching expression="otu_removed.*:\s0" />
5
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70 <has_text_matching expression="otu_kept.*:\s52" />
0
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71 </assert_contents>
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72 </output>
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73 </test>
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74 </tests>
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75 <help>
7
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76 @HELP_LOGO@
0
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77
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78 .. class:: infomark page-header h2
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79
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80 What it does
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81
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82 Creation of a multiple alignment of OTUs with `Mafft &lt;http://mafft.cbrc.jp/alignment/software&gt;`_.
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83 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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84
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85 .. class:: infomark page-header h2
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86
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87 Inputs/Outputs
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88
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89 .. class:: h3
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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 Input
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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 **OTUs fasta file**:
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94
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95 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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96 Careful: FROGS Tree works only with less than 10 000 sequences!
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97
0
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98 .. image:: static/images/FROGS_tree_otufile.png
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99
0
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100 **OTUs biom file**:
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101
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102 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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103 This file can be obtained in particular with the FROGS pipeline.
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104
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105 .. class:: h3
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106
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107 Outputs
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108
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109 **Newick file** (tree.nwk):
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110
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111 The phylogenetic tree in Newick format (format `nwk or nhx &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_).
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112
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113 .. image:: static/images/FROGS_nwk_treefile.png
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114
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115 **Html file** (summary.html):
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116
0
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117 The summary file describing which OTUs are contained or not in the phylogenetic tree.
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118
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119 .. class:: infomark page-header h2
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120
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121 @HELP_CONTACT@
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122
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123
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124
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125 </help>
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126
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127 <citations>
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128 <expand macro="citations" />
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129 </citations>
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130
0
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131 </tool>