Mercurial > repos > frogs > frogs_2_0_0
annotate tree.xml @ 0:76c750c5f0d1 draft default tip
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
author | frogs |
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date | Thu, 25 Oct 2018 05:01:13 -0400 |
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0
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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1 <?xml version="1.0"?> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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2 <!-- |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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3 # Copyright (C) 2017 INRA |
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4 # |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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5 # This program is free software: you can redistribute it and/or modify |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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6 # it under the terms of the GNU General Public License as published by |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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7 # the Free Software Foundation, either version 3 of the License, or |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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8 # (at your option) any later version. |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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9 # |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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10 # This program is distributed in the hope that it will be useful, |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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13 # GNU General Public License for more details. |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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14 # |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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15 # You should have received a copy of the GNU General Public License |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>. |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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17 --> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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18 <tool id="FROGS_Tree" name="FROGS Tree" version="1.0.0"> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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19 <description>Reconstruction of phylogenetic tree </description> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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20 <requirements> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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21 <requirement type="package" version="2.0.1">frogs</requirement> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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22 </requirements> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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23 <stdio> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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24 <exit_code range="1:" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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25 <exit_code range=":-1" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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26 </stdio> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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27 <command>tree.py |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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28 --input-otu $input_otu |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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29 #if $template.fileTemplate |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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30 --template-pynast ${template.template_pynast} |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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31 #end if |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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32 --biomfile $biomfile |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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33 --nb-cpus $nb_cpus |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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34 --out-tree $out_tree |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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35 --html $html |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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36 </command> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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37 <inputs> |
76c750c5f0d1
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38 <!-- Files --> |
76c750c5f0d1
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39 <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"> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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40 <validator type="empty_field" message="This parameter is required." /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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41 </param> |
76c750c5f0d1
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42 <conditional name="template"> |
76c750c5f0d1
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43 <param name="fileTemplate" type="boolean" label="Do you have the template alignment file ?" help="If yes, precise the template multi-alignment file." optional="false" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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44 <when value="false"></when> |
76c750c5f0d1
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45 <when value="true"> |
76c750c5f0d1
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46 <param format="fasta" name="template_pynast" type="data" label="Template alignment file" help="Template multi-alignment file (format: fasta)." optional="false" /> |
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47 </when> |
76c750c5f0d1
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48 </conditional> |
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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 <!-- Parameter --> |
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53 <param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" /> |
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54 </inputs> |
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55 <outputs> |
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56 <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/> |
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57 <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/> |
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58 </outputs> |
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59 <tests> |
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60 <test> |
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61 <param name="input_otu" value="references/04-filters.fasta"/> |
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62 <conditional name="template"> |
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63 <param name="fileTemplate" value="false"/> |
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64 </conditional> |
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65 <param name="biomfile" value="references/04-affiliation.biom"/> |
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66 <output name="out_tree" value="references/10b-tree.nwk"/> |
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67 </test> |
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68 </tests> |
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69 <help> |
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70 .. image:: static/images/FROGS_logo.png |
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71 :height: 144 |
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72 :width: 110 |
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73 |
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74 .. class:: infomark page-header h2 |
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75 |
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76 What it does |
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77 |
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78 Creation of a multiple alignment of OTUs with `PyNAST <http://biocore.github.io/pynast/>`_ (if you have an alignment template file) or with `Mafft <http://mafft.cbrc.jp/alignment/software>`_ (if you have not an aligned template file). |
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79 And creation of a phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_. |
76c750c5f0d1
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80 |
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81 .. class:: infomark page-header h2 |
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82 |
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83 Inputs/Outputs |
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84 |
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85 .. class:: h3 |
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86 |
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87 Input |
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88 |
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89 **OTUs fasta file**: |
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90 |
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91 The OTUs sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). |
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92 Careful: FROGS Tree works only with less than 10 000 sequences! |
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93 |
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94 .. image:: static/images/frogs_tree_otufile.png |
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95 |
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96 **(optional) Template alignment file**: |
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97 |
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98 A pre-aligned database of sequences (the “template” sequence) (format `multiple alignement <https://en.wikipedia.org/wiki/Multiple_sequence_alignment>`_). |
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99 |
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100 .. image:: static/images/frogs_tree_templatefile.png |
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101 |
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102 **OTUs biom file**: |
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103 |
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104 The OTUs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). |
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105 This file can be obtained in particular with the FROGS pipeline. |
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106 |
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107 .. class:: h3 |
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108 |
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109 Outputs |
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110 |
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111 **Newick file** (tree.nwk): |
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112 |
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113 The phylogenetic tree in Newick format (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_). |
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114 |
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115 .. image:: static/images/nwk_treefile.png |
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116 |
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117 **Html file** (summary.html): |
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118 |
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119 The summary file describing which OTUs are contained or not in the phylogenetic tree (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). |
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120 |
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121 .. class:: infomark page-header h2 |
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122 |
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123 **Contact** |
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124 |
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125 Contacts: frogs@inra.fr |
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126 |
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127 Repository: https://github.com/geraldinepascal/FROGS |
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128 |
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129 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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130 |
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131 Depending on the help provided you can cite us in acknowledgements, references or both. |
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132 |
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133 </help> |
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134 <citations> |
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135 <citation type="doi">10.7287/peerj.preprints.386v1</citation> |
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136 </citations> |
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137 </tool> |