Commit 73a16a18 authored by khalid's avatar khalid
Browse files

Add Frogs biom 2 tsv

parent be068df3
rule <step_name>__FROGS_biom_to_tsv:
input:
**<step_name>__FROGS_biom_to_tsv_inputs(),
output:
abundance_file = config["results_dir"]+'/'+config["<step_name>__FROGS_biom_to_tsv_output_dir"]+'/tax_affiliation.tsv',
log: config["results_dir"]+'/logs/' + config["<step_name>__FROGS_biom_to_tsv_output_dir"] + '/FROGS_biom_to_tsv_log.txt',
params:
command = config["<step_name>__FROGS_biom_to_tsv_command"],
outDir = config["results_dir"]+'/'+config["<step_name>__FROGS_biom_to_tsv_output_dir"],
shell: """
{params.command} -b {input.biom} -t {output.abundance_file}
"""
\ No newline at end of file
{
id: FROGS_biom_to_tsv,
name: FROGS biom2tsv,
article: 10.1093/bib/bbab318,
website: "http://frogs.toulouse.inrae.fr/",
git: "https://github.com/geraldinepascal/FROGS",
description: "Adding taxonomic affiliation in abundance file",
version: "3.2.3",
documentation: "http://frogs.toulouse.inrae.fr/html/commands_utax.html",
multiqc: "custom",
commands:
[
{
name: FROGS_biom_to_tsv,
command: "/opt/biotools/FROGS-3.2.3/app/biom_to_tsv.py",
category: "FROGS",
output_dir: FROGS_biom_to_tsv,
inputs:
[
#{ name: fasta, type: "fasta_file", description: "the sequences in fasta format"},
{ name: biom, type: "biom", description: "the abundance of each OTU in each sample"}
],
outputs:
[
{ name: "abundance_file", file: "tax_affiliation.tsv", type: "tsv", description: "output file with the abundance and metadata (tsv)"},
],
options:
[
],
},
],
install:
{
perl: [
"sudo apt-get install python3 perl" # deja installé
],
frogs: [
"cd /opt/biotools",
"wget https://github.com/geraldinepascal/FROGS/archive/v3.2.3.tar.gz",
"tar -zxvf v3.2.3.tar.gz",
"cd FROGS-3.2.3",
"mkdir bin"
],
scipy: [
"apt-get install python3-scipy" # demande confirmation
],
},
citations: {
frogs: [
" Maria Bernard, Olivier Rué, Mahendra Mariadassou and Géraldine Pascal; FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers, Briefings in Bioinformatics 2021, 10.1093/bib/bbab318 "
]
}
}
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