Commit 563546c1 authored by khalid's avatar khalid
Browse files

Add RDPclassifier

parent 73a16a18
......@@ -15,7 +15,7 @@ rule <step_name>__FROGS_affiliation:
taxfile = config["<step_name>__FROGS_affiliation_reference_fasta"]+"/train_set.fasta",
yamlfile = config["<step_name>__FROGS_affiliation_reference_fasta"]+"/info.yaml",
# taxonomic_ranks = "-t Domain Phylum Class Order Family Genus Species",
#rdp = "--rdp "+config["<step_name>__FROGS_affiliation_rdp"] if config["<step_name>__FROGS_affiliation_rdp"] else "",
rdp = " --rdp " if config["<step_name>__FROGS_affiliation_rdp"] else "",
threads:
config["<step_name>__FROGS_affiliation_threads"],
shell: """
......@@ -39,5 +39,5 @@ rule <step_name>__FROGS_affiliation:
{params.cmdStat} -i {output.abundance_file} --tax-consensus-tag 'blast_taxonomy' --multiple-tag 'blast_affiliations' -o {params.outDir}/affiliations_stat.html ;
echo \"2\t./{params.stepDir}/affiliations_stat.html\" >> {params.outDir}/text.generic.tsv
"""
# {params.rdp} \
#{params.taxonomic_ranks} \
\ No newline at end of file
......@@ -2,7 +2,7 @@
id: FROGS_affiliation,
name: FROGS affiliation,
article: 10.1093/bib/bbab318,
website: "http://f rogs.toulouse.inrae.fr/",
website: "http://frogs.toulouse.inrae.fr/",
git: "https://github.com/geraldinepascal/FROGS",
description: "Adding taxonomic affiliation in abundance file",
version: "3.2.3",
......@@ -42,7 +42,7 @@
prefix: --rdp,
type: checkbox,
value: False,
label: "[NOT AVAILABLE] Also perform RDP assignation ?",
label: "Also perform RDP assignation ?",
},
{
name: FROGS_affiliation_reference_fasta,
......@@ -108,6 +108,18 @@
# add to FROGS
"ln -s /opt/biotools/FROGS-3.2.3/bin/EMBOSS-6.6.0/emboss/needleall /opt/biotools/FROGS-3.2.3/libexec/."
],
ant : ["apt-get install ant"],
RDPclasifier: [
"cd /opt/biotools/",
"git clone https://github.com/rdpstaff/RDPTools.git",
"cd RDPTools",
"git checkout 2.0.3",
"git submodule init",
"git submodule update",
"make",
# add to FROGS
"ln -s opt/biotools/RDPTools/classifier.jar /opt/biotools/FROGS-3.2.3/libexec/."
],
},
data: [
{
......
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