FROGS stat

affiliation.smk

@@ -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}"

global.smk

@@ -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"