Mercurial > repos > frogs > frogs_2_0_0

annotate tsv_to_biom.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) 2016 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_tsv_to_biom" name="FROGS TSV_to_BIOM" version="2.0.0">
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19 <description>Converts a TSV file in a BIOM file.</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 tsv_to_biom.py
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29 --input-tsv $tsv_file
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30 --output-biom $biom_file
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31 #if $multi_affi_file
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32 --input-multi-affi $multi_affi_file
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33 #end if
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34 #if $extract_fasta
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35 --output-fasta $sequence_file
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36 #end if
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37 </command>
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38 <inputs>
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39 <!-- Files -->
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40 <param format="tabular" name="tsv_file" type="data" label="Abundance TSV File" help="Your FROGS abundance TSV file. Take care to keep original column names." optional="false"/>
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41 <param format="tabular" name="multi_affi_file" type="data" label="Multi_hits TSV File" help="TSV file describing multi_hit blast results." optional="true" />
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42 <!-- Parameters -->
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43 <param name="extract_fasta" type="boolean" label="Extract seeds in FASTA file" help="If there is a 'seed_sequence' column in your TSV table, you can extract seed sequences in a separated FASTA file." />
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44 </inputs>
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45 <outputs>
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46 <data format="biom1" name="biom_file" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" />
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47 <data format="fasta" name="sequence_file" label="${tool.name}: sequences.fasta" from_work_dir="seed.fasta" >
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48 <filter>extract_fasta</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="tsv_file" value="references/07-biom2tsv.tsv" />
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54 <param name="multi_affi_file" value="references/07-biom2tsv.multi" />
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55 <param name="extract_fasta" value="true"/>
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56 <output name="biom_file" file="references/09-tsv2biom.biom" compare="sim_size" delta="0"/>
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57 <output name="sequence_file" file="references/09-tsv2biom.fasta" />
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58 </test>
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59 </tests>
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60 <help>
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61 .. image:: static/images/FROGS_logo.png
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62 :height: 144
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63 :width: 110
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64
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65
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66 .. class:: infomark page-header h2
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67
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68 What it does
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69
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70 This tool converts a TSV file in a BIOM file.
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71
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72 .. class:: h3
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73
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74 Inputs
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75
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76 **Abundance file**:
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77
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78 The table with abundances each cluster in each sample and other details conerning the cluster (format TSV).
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79
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80 Authorised column names : rdp_tax_and_bootstrap, blast_taxonomy, blast_subject, blast_perc_identity, blast_perc_query_coverage, blast_evalue, blast_aln_length, seed_id, seed_sequence, observation_name, observation_sum
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81
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82 **Multiple affiliation file**:
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83
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84 The file that stores the multiple blast hits.
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85
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86 .. class:: h3
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87
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88 Outputs
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89
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90 **Abundance file**:
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91
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92 The abundance of each cluster in each sample and their metadata (format `BIOM &lt;http://biom-format.org/&gt;`_).
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93
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94 **Sequence file [optional]**:
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95
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96 By checking the "Extract seed FASTA file" option, the sequences will be extract from TSV to create a file in `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_ format.
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97 For this option, be sure that your TSV file contains the seed_sequence column.
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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 TSV_to_BIOM detects any metadata (columns before "observation_name") and names of samples (columns after "observation_sum").
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105
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106 Then it reconstructs the BIOM abundance file : for each "observation_name" it adds the associated metadata and the count of samples.
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107
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108 If blast_taxonomy is included in metadata and if blast_subject is equal to "multi-subject", it parses multi_hit TSV file. Then it extracts the list of blast_affiliations that contains the non ambiguous blast_taxonomy.
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109
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110
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111
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112 .. class:: infomark page-header h2
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113
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114 Advices
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115
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116 This tool is usefull if you have modified your abundance TSV file and that you want to generate rarefaction curve or sunburst with the FROGS affiliation_stat tool.
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117
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118 If you modify your abundance TSV file
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119
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120 * -do not modify column names
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121 * -do not remove columns
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122 * -take care to choose a taxonomy available in your multi_hit TSV file
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123 * -if you delete lines of the multi_hit file, take care to not remove a complete cluster whithout removing all "multi tags" in you abundance TSV file.
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124 * -if you want to rename a taxon level (ex : genus "Ruminiclostridium 5;" to genus "Ruminiclostridium;"), do not forget to modify also your multi_hit TSV file.
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125
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126 ----
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127
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128 **Contact**
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129
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130 Contacts: frogs@inra.fr
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131
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132 Repository: https://github.com/geraldinepascal/FROGS
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133
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134 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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135
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136 Depending on the help provided you can cite us in acknowledgements, references or both.
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137 </help>
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138 <citations>
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139 <citation type="doi">10.1093/bioinformatics/btx791</citation>
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140 <citation type="doi">10.1128/AEM.01043-13</citation>
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141 <citation type="doi">10.14806/ej.17.1.200</citation>
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142 <citation type="doi">10.1093/bioinformatics/btr507</citation>
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143 </citations>
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144
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145 </tool>