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annotate biom_to_stdBiom.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_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="1.1.0">
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19 <description>Converts a FROGS BIOM in fully compatible BIOM.</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 biom_to_stdBiom.py
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29 --input-biom $input_biom
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30 --output-biom $output_biom
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31 --output-metadata $output_metadata
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32 </command>
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33 <inputs>
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34 <!-- Files -->
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35 <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The FROGS BIOM file to convert (format: BIOM)." optional="false" />
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36 </inputs>
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37 <outputs>
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38 <data format="biom1" name="output_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom"/>
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39 <data format="tabular" name="output_metadata" label="${tool.name}: blast_metadata.tsv" from_work_dir="blast_metadata.tsv" />
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="input_biom" value="references/04-affiliation.biom"/>
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44 <output name="output_biom" value="references/08-affiliation_std.biom"/>
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45 <output name="output_metadata" value="references/08-affiliation_multihit.tsv"/>
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46 </test>
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47 </tests>
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48 <help>
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49
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50 .. image:: static/images/FROGS_logo.png
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51 :height: 144
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52 :width: 110
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53
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55 .. class:: infomark page-header h2
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56
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57 What it does
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58
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59 Converts a BIOM generated by FROGS in generic BIOM.
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60
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61 The detailed blast affiliations can trigger problem with tools like Qiime. This tool extracts the problematic metadata in a second file and writes a BIOM usable in every tools using BIOM.
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62
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63 .. class:: h3
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64
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65 Inputs
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66
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67 **Abundance file**:
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68
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69 The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
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70
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71 .. class:: h3
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73 Outputs
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75 **Abundance file**:
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76
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77 The abundance without the incompatible metadata (format `BIOM &lt;http://biom-format.org/&gt;`_).
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79 **Blast metadata file**:
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80
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81 The details for each alignment on clusters (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).
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84 .. class:: infomark page-header h2
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86 How it works
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88 FROGS BIOM to std BIOM extracts the blast alignment metadata in a second file, write a BIOM usable in every tools using BIOM and defined the taxonomy provided by blast as main taxonomy.
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92 ----
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93
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94 **Contact**
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95
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96 Contacts: frogs@inra.fr
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97
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98 Repository: https://github.com/geraldinepascal/FROGS
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99
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100 Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
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101
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102 Depending on the help provided you can cite us in acknowledgements, references or both.
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103 </help>
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104 <citations>
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105 <citation type="doi">10.7287/peerj.preprints.386v1</citation>
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106 </citations>
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107 </tool>