comparison tsv_to_biom.xml @ 0:76c750c5f0d1 draft default tip

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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-1:000000000000 0:76c750c5f0d1
1 <?xml version="1.0"?>
2 <!--
3 # Copyright (C) 2016 INRA
4 #
5 # This program is free software: you can redistribute it and/or modify
6 # it under the terms of the GNU General Public License as published by
7 # the Free Software Foundation, either version 3 of the License, or
8 # (at your option) any later version.
9 #
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
14 #
15 # You should have received a copy of the GNU General Public License
16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
17 -->
18 <tool id="FROGS_tsv_to_biom" name="FROGS TSV_to_BIOM" version="2.0.0">
19 <description>Converts a TSV file in a BIOM file.</description>
20 <requirements>
21 <requirement type="package" version="2.0.1">frogs</requirement>
22 </requirements>
23 <stdio>
24 <exit_code range="1:" />
25 <exit_code range=":-1" />
26 </stdio>
27 <command>
28 tsv_to_biom.py
29 --input-tsv $tsv_file
30 --output-biom $biom_file
31 #if $multi_affi_file
32 --input-multi-affi $multi_affi_file
33 #end if
34 #if $extract_fasta
35 --output-fasta $sequence_file
36 #end if
37 </command>
38 <inputs>
39 <!-- Files -->
40 <param format="tabular" name="tsv_file" type="data" label="Abundance TSV File" help="Your FROGS abundance TSV file. Take care to keep original column names." optional="false"/>
41 <param format="tabular" name="multi_affi_file" type="data" label="Multi_hits TSV File" help="TSV file describing multi_hit blast results." optional="true" />
42 <!-- Parameters -->
43 <param name="extract_fasta" type="boolean" label="Extract seeds in FASTA file" help="If there is a 'seed_sequence' column in your TSV table, you can extract seed sequences in a separated FASTA file." />
44 </inputs>
45 <outputs>
46 <data format="biom1" name="biom_file" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" />
47 <data format="fasta" name="sequence_file" label="${tool.name}: sequences.fasta" from_work_dir="seed.fasta" >
48 <filter>extract_fasta</filter>
49 </data>
50 </outputs>
51 <tests>
52 <test>
53 <param name="tsv_file" value="references/07-biom2tsv.tsv" />
54 <param name="multi_affi_file" value="references/07-biom2tsv.multi" />
55 <param name="extract_fasta" value="true"/>
56 <output name="biom_file" file="references/09-tsv2biom.biom" compare="sim_size" delta="0"/>
57 <output name="sequence_file" file="references/09-tsv2biom.fasta" />
58 </test>
59 </tests>
60 <help>
61 .. image:: static/images/FROGS_logo.png
62 :height: 144
63 :width: 110
64
65
66 .. class:: infomark page-header h2
67
68 What it does
69
70 This tool converts a TSV file in a BIOM file.
71
72 .. class:: h3
73
74 Inputs
75
76 **Abundance file**:
77
78 The table with abundances each cluster in each sample and other details conerning the cluster (format TSV).
79
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
81
82 **Multiple affiliation file**:
83
84 The file that stores the multiple blast hits.
85
86 .. class:: h3
87
88 Outputs
89
90 **Abundance file**:
91
92 The abundance of each cluster in each sample and their metadata (format `BIOM &lt;http://biom-format.org/&gt;`_).
93
94 **Sequence file [optional]**:
95
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.
97 For this option, be sure that your TSV file contains the seed_sequence column.
98
99
100 .. class:: infomark page-header h2
101
102 How it works
103
104 FROGS TSV_to_BIOM detects any metadata (columns before "observation_name") and names of samples (columns after "observation_sum").
105
106 Then it reconstructs the BIOM abundance file : for each "observation_name" it adds the associated metadata and the count of samples.
107
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.
109
110
111
112 .. class:: infomark page-header h2
113
114 Advices
115
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.
117
118 If you modify your abundance TSV file
119
120 * -do not modify column names
121 * -do not remove columns
122 * -take care to choose a taxonomy available in your multi_hit TSV file
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.
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.
125
126 ----
127
128 **Contact**
129
130 Contacts: frogs@inra.fr
131
132 Repository: https://github.com/geraldinepascal/FROGS
133
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
135
136 Depending on the help provided you can cite us in acknowledgements, references or both.
137 </help>
138 <citations>
139 <citation type="doi">10.1093/bioinformatics/btx791</citation>
140 <citation type="doi">10.1128/AEM.01043-13</citation>
141 <citation type="doi">10.14806/ej.17.1.200</citation>
142 <citation type="doi">10.1093/bioinformatics/btr507</citation>
143 </citations>
144
145 </tool>