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annotate normalisation.xml @ 0:76c750c5f0d1 draft default tip

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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
author frogs
date Thu, 25 Oct 2018 05:01:13 -0400
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0
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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="2.0.0">
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19 <description>Normalize OTUs abundance.</description>
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20 <requirements>
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21 <requirement type="package" version="2.0.1">frogs</requirement>
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22 </requirements>
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23 <!--stdio>
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24 <exit_code range="1:" />
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25 <exit_code range=":-1" />
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26 </stdio-->
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27 <command>
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28 normalisation.py
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29 --input-biom $input_biom
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30 --input-fasta $input_fasta
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31 --num-reads $num_reads
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32 --output-biom $output_biom
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33 --output-fasta $output_fasta
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34 --summary-file $summary_file
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35 </command>
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36 <inputs>
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37 <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalize (format: fasta)." />
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38 <param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalize (format: BIOM)." />
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39 <param name="num_reads" type="integer" optional="false" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
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40 </inputs>
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41 <outputs>
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42 <data format="fasta" name="output_fasta" label="${tool.name}: normalized.fasta" from_work_dir="normalized.fasta" />
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43 <data format="biom1" name="output_biom" label="${tool.name}: normalized.biom" from_work_dir="normalized.biom" />
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44 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="input_fasta" value="references/04-filters.fasta"/>
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49 <param name="input_biom" value="references/04-affiliation.biom"/>
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50 <param name="num_reads" value="100"/>
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51 <output name="summary_file" file="references/normalisation_report.html" compare="sim_size" delta="0" />
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52 </test>
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53 </tests>
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54 <help>
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55
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56 .. image:: static/images/FROGS_logo.png
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57 :height: 144
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58 :width: 110
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59
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60
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61 .. class:: infomark page-header h2
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62
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63 What it does
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64
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65 This tool keeps, in each sample, the same number of elements by random sampling.
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66
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67 .. class:: infomark page-header h2
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68
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69 Inputs/outputs
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70
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71 .. class:: h3
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72
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73 Inputs
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74
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75 **Sequence file**:
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76
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77 The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
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78
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79 **Abundance file**:
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80
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81 The abundance of each OTU in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
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82
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83 .. class:: h3
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84
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85 Outputs
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86
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87 **Sequence file** (normalised_seed.fasta):
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88
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89 The normalised sequences file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
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90
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91 **Abundance file** (normalised_abundance.biom):
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92
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93 The normalised abundance file (format `BIOM &lt;http://biom-format.org/&gt;`_).
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94
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95 **Summary file** (report.html):
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96
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97 Information about discarded data (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
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98
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99
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100 .. class:: infomark page-header h2
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101
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102 Advices
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103
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104 The number specified in "Number of reads" must be smaller than each total number of sequences by sample.
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105
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106
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107 ----
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108
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109 **Contact**
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110
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111 Contacts: frogs@inra.fr
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112
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113 Repository: https://github.com/geraldinepascal/FROGS
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114
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115 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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116
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117 Depending on the help provided you can cite us in acknowledgements, references or both.
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118 </help>
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119 <citations>
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120 <citation type="doi">10.7287/peerj.preprints.386v1</citation>
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121 </citations>
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122 </tool>