Mercurial > repos > frogs > frogs_2_0_0
annotate biom_to_tsv.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) 2015 INRA |
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4 # |
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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 |
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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. |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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9 # |
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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, |
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of |
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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 # |
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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_biom_to_tsv" name="FROGS BIOM to TSV" version="2.1.0"> |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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19 <description>Converts a BIOM file in TSV file.</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> |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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23 <stdio> |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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24 <exit_code range="1:" /> |
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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> |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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28 biom_to_tsv.py |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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29 --input-biom $biom_file |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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30 #if $sequence_file |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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31 --input-fasta $sequence_file |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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32 #end if |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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33 --output-tsv $tsv_file |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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34 #if $extract_multi_align |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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35 --output-multi-affi $multi_affi_file |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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36 #end if |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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37 </command> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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38 <inputs> |
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39 <!-- Files --> |
76c750c5f0d1
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40 <param format="biom1" name="biom_file" type="data" label="Abundance file" help="The BIOM file to convert (format: BIOM)." optional="false" /> |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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41 <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta). If you use this option the sequences will be add in TSV." optional="true" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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42 <!-- Parameters --> |
76c750c5f0d1
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43 <param name="extract_multi_align" type="boolean" label="Extract multi-alignments" help="If you have used FROGS affiliation on your data, you can extract information about multiple alignements in a second TSV." /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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44 </inputs> |
76c750c5f0d1
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45 <outputs> |
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46 <data format="tabular" name="tsv_file" label="${tool.name}: abundance.tsv" from_work_dir="abundance.tsv"/> |
76c750c5f0d1
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47 <data format="tabular" name="multi_affi_file" label="${tool.name}: multi_hits.tsv" from_work_dir="multi_hits.tsv" > |
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48 <filter>extract_multi_align</filter> |
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49 </data> |
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50 </outputs> |
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51 <tests> |
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52 <test> |
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53 <param name="biom_file" value="references/04-affiliation.biom"/> |
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54 <param name="sequence_file" value="references/04-filters.fasta"/> |
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55 <param name="extract_multi_align" value="true"/> |
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56 <output name="tsv_file" value="references/07-biom2tsv.tsv"/> |
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57 <output name="multi_affi_file" value="references/07-biom2tsv.multi"/> |
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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 .. image:: static/images/FROGS_logo.png |
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63 :height: 144 |
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64 :width: 110 |
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65 |
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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 What it does |
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70 |
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71 Converts a BIOM file in TSV file. |
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72 |
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73 .. class:: h3 |
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74 |
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75 Inputs |
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76 |
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77 **Abundance file**: |
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78 |
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79 The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_). |
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80 |
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81 **Sequence file [optional]**: |
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82 |
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83 The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). |
76c750c5f0d1
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84 |
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85 .. class:: h3 |
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86 |
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87 Outputs |
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88 |
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89 **Abundance file**: |
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90 |
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91 The abundance of each cluster in each sample and theirs metadata (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). |
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92 |
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93 If you add the sequences file, this information is added for each cluster. |
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94 |
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95 **Multiple affiliation file**: |
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96 |
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97 If you have used *FROGS affiliation* on your data, each OTU can have several affiliations: several alignments with same score on reference database. The multiple affiliation file contains details on these possibles affiliations (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). |
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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 How it works |
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103 |
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104 FROGS Biom to Tsv will search if any metadata are available, and the OTU sequence if fasta file is precised. Then it will extract the OTU name, sum the abundance, and extract the detailed abundance for each sample. Finally it will write all these fields separated by tabulation in the TSV file. |
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105 |
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106 |
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107 .. class:: infomark page-header h2 |
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108 |
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109 Advices |
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110 |
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111 This output tsv file is easily readable in any spreadsheet software. Be aware that these software have a number of line limit (1 048 576 for Excel and LibreOffice calc ate least). If you have more OTU, use **FROGS Filters** to extract for example the most abundant OTU before converting your BIOM abundance table in TSV file. |
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112 |
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113 |
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114 ---- |
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115 |
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116 **Contact** |
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117 |
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118 Contacts: frogs@inra.fr |
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119 |
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120 Repository: https://github.com/geraldinepascal/FROGS |
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121 |
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122 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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123 |
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124 Depending on the help provided you can cite us in acknowledgements, references or both. |
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125 </help> |
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126 <citations> |
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127 <citation type="doi">10.7287/peerj.preprints.386v1</citation> |
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128 </citations> |
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129 </tool> |