Commit ea533335 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

FROGS stat

parent 46c66daf
......@@ -19,3 +19,61 @@ rule affiliation:
"--input-fasta {input.fasta} "
"--summary {output.html} "
"--output-biom {output.biom}"
rule stats:
input:
biom = "work/FROGS/affiliation.biom"
output:
html_cluster = "work/FROGS/clusters_metrics.html",
html_affiliations = "work/FROGS/affiliations_metrics.html"
shell:
"clusters_stat.py "
"--input-biom {input.biom} "
"--output-file {output.html_cluster}"
" ; "
"affiliations_stat.py "
"--input-biom {input.biom} "
"--output-file {output.html_affiliations} "
"--taxonomic-ranks Domain Phylum Class Order Family Genus Species "
"--rarefaction-ranks Genus "
"--multiple-tag blast_affiliations "
"--tax-consensus-tag blast_taxonomy "
"--identity-tag perc_identity "
"--coverage-tag perc_query_coverage"
rule tree:
input:
fasta = "work/dada/seqtab.fasta",
biom = "work/FROGS/affiliation.biom"
output:
html = "work/FROGS/tree.html",
nwk = "work/FROGS/tree.nwk"
threads:
config["THREADS"]
shell:
"/projet/galaxyprod/galaxy/tools/FROGS/app/tree.py "
"--nb-cpus {threads} "
"--input-otu {input.fasta} "
"--biomfile {input.biom} "
"--html {output.html} "
"--out-tree {output.nwk}"
rule stdBIOM:
input:
biom = "work/FROGS/affiliation.biom"
output:
biom = "work/FROGS/abundance.biom",
tsv = "work/FROGS/multihits.tsv"
shell:
"biom_to_stdBiom.py "
"--input-biom {input.biom} "
"--output-biom {output.biom} "
"--output-metadata {output.tsv}"
rule copy:
input:
"work/FROGS/{file}"
output:
"report/{file}"
shell:
"cp -uv {input} {output}"
......@@ -9,7 +9,10 @@ rule all:
expand("work/dada/{sample}.rds", sample=SAMPLES),
"work/dada/seqtab.fasta",
"work/dada/seqtab.tsv",
"work/FROGS/affiliation.biom"
"work/FROGS/affiliation.biom",
"report/clusters_metrics.html",
"report/affiliations_metrics.html",
"report/abundance.biom"
include: "quality.smk"
include: "preprocess.smk"
......
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