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annotate normalisation.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) 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_normalisation" name="FROGS Abundance normalisation" version="@TOOL_VERSION@+galaxy2">
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19 <description>Normalise OTUs abundance.</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
0
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27 <stdio>
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28 <exit_code range="1:" />
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29 <exit_code range=":-1" />
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30 </stdio>
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31 <command>
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32 normalisation.py
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33 --input-biom '$input_biom'
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34 --input-fasta '$input_fasta'
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35 --num-reads $num_reads
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36 --output-biom '$output_biom'
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37 --output-fasta '$output_fasta'
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38 --summary-file '$summary_file'
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39 </command>
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40 <inputs>
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41 <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." />
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42 <param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." />
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43 <param name="num_reads" type="integer" optional="false" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
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44 </inputs>
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45 <outputs>
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46 <data format="fasta" name="output_fasta" label="${tool.name}: normalised_sequences.fasta" from_work_dir="normalised.fasta" />
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47 <data format="biom1" name="output_biom" label="${tool.name}: normalised_abundance.biom" from_work_dir="normalised.biom" />
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48 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="input_fasta" value="references/08-affiliation_postprocessed.fasta"/>
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53 <param name="input_biom" value="references/08-affiliation_postprocessed.biom"/>
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54 <param name="num_reads" value="100"/>
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55 <output name="summary_file" file="references/09-normalisation.html" compare="sim_size" delta="0" />
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56 <output name="summary_file" file="references/09-normalisation.html" compare="diff" lines_diff="4" />
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57 <output name="output_fasta" file="references/09-normalisation.fasta" compare="diff" lines_diff="12" />
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58 </test>
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59 </tests>
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60 <help>
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61
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62 @HELP_LOGO@
0
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63
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64 .. class:: infomark page-header h2
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65
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66 What it does
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67
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68 This tool keeps, in each sample, the same number of elements by random sampling.
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69
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70 .. class:: infomark page-header h2
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71
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72 Inputs/outputs
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73
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74 .. class:: h3
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75
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76 Inputs
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78 **Sequence file**:
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79
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80 The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
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81
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82 **Abundance file**:
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83
0
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84 The abundance of each OTU in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
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85
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86 .. class:: h3
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88 Outputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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89
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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90 **Sequence file** (normalised_seed.fasta):
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 The normalised sequences 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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93
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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94 **Abundance file** (normalised_abundance.biom):
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 The normalised abundance file (format `BIOM &lt;http://biom-format.org/&gt;`_).
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 **Summary file** (report.html):
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 Information about discarded data (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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101
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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102
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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103 .. 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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104
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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105 Advices
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 The number specified in "Number of reads" must be smaller than each total number of sequences by sample.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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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
7
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110 @HELP_CONTACT@
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
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111
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112 </help>
7
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113
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114 <citations>
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115 <expand macro="citations" />
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116 </citations>
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117
0
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118 </tool>