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annotate tree.xml @ 9:7bf54edaba24 draft

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
author oinizan
date Thu, 12 May 2022 10:44:30 +0000
parents 76dcbe930b1d
children 6540a5092c6e
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7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
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1 <tool id="FROGS_Tree" name="FROGS Tree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">
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2 <description>Reconstruction of phylogenetic tree </description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="7.407">mafft</requirement>
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8 <requirement type="package" version="2.1.9">fasttree</requirement>
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9 <requirement type="package" version="4.1.2">r-base</requirement>
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10 <requirement type="package" version="4.1">r-essentials</requirement>
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11 <requirement type="package" version="2.7.0">r-phangorn</requirement>
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12 </expand>
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13 <command detect_errors="exit_code">
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14 tree.py
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15 --input-sequences '$input_otu'
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16 --biom-file '$biomfile'
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17 @CPUS@
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18 --out-tree '$out_tree'
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19 --html '$html'
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20 </command>
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21 <inputs>
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22 <!-- Files -->
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23 <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!"/>
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24 <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: BIOM)"/>
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25 </inputs>
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26 <outputs>
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27 <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk" />
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28 <data format="html" name="html" label="${tool.name}: report.html" from_work_dir="summary.html" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input_otu" value="references/09-normalisation.fasta" />
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33 <param name="biomfile" value="references/09-normalisation.biom" />
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34 <output name="out_tree" value="references/15-tree-mafft.nwk" compare="sim_size" delta="30" />
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35 <output name="html" value="references/15-tree-mafft.html" compare="diff" lines_diff="2" />
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36 <output name="html" value="references/15-tree-mafft.html" compare="sim_size" delta="30" />
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37 <output name="html">
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38 <assert_contents>
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39 <has_text_matching expression="FROGS\sTree" />
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40 <has_text_matching expression="abundance_removed.*:\s0" />
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41 <has_text_matching expression="abundance_kept.*:\s300" />
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42 <has_text_matching expression="otu_removed.*:\s0" />
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43 <has_text_matching expression="otu_kept.*:\s50" />
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44 </assert_contents>
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45 </output>
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46 </test>
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47 </tests>
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48 <help>
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49 @HELP_LOGO@
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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 Creation of a multiple alignment of OTUs with `Mafft &lt;http://mafft.cbrc.jp/alignment/software&gt;`_.
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56 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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57
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58 .. class:: infomark page-header h2
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59
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60 Inputs/Outputs
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61
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62 .. class:: h3
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64 Input
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65
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66 **OTUs fasta file**:
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67
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68 The OTUs sequence file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
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69 Careful: FROGS Tree works only with less than 10 000 sequences!
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70
0
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71 .. image:: static/images/FROGS_tree_otufile.png
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72
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73 **OTUs biom file**:
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74
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75 The OTUs biom file (format `biom1 &lt;http://biom-format.org/documentation/format_versions/biom-1.0.html&gt;`_).
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76 This file can be obtained in particular with the FROGS pipeline.
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78 .. class:: h3
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80 Outputs
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81
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82 **Newick file** (tree.nwk):
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83
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84 The phylogenetic tree in Newick format (format `nwk or nhx &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_).
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86 .. image:: static/images/FROGS_nwk_treefile.png
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87
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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88 **Html file** (summary.html):
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76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
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89
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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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90 The summary file describing which OTUs are contained or not in the phylogenetic tree.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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91
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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92 .. class:: infomark page-header h2
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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93
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76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
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94 @HELP_CONTACT@
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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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95
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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96
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 </help>
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7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
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99 <expand macro="citations" />
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100 </tool>