Commit 708f85f8 authored by khalid's avatar khalid
Browse files

Add html output to report

parent 2a9865aa
...@@ -7,15 +7,33 @@ ...@@ -7,15 +7,33 @@
command = config["<step_name>__FROGS_phyloseq_stats_command"], command = config["<step_name>__FROGS_phyloseq_stats_command"],
outDir = config["results_dir"]+'/'+config["<step_name>__FROGS_phyloseq_stats_output_dir"], outDir = config["results_dir"]+'/'+config["<step_name>__FROGS_phyloseq_stats_output_dir"],
varExp = config["<step_name>__FROGS_phyloseq_stats_varExp"], varExp = config["<step_name>__FROGS_phyloseq_stats_varExp"],
stepDir = config["<step_name>__FROGS_phyloseq_stats_output_dir"],
shell: """ shell: """
cd {params.outDir}; cd {params.outDir};
{params.command}/tree.py -i {input.otu_sequence_file} -b {input.biom_file}; {params.command}/tree.py -i {input.otu_sequence_file} -b {input.biom_file};
echo \"1\t./{params.stepDir}/tree.html\" > {params.outDir}/text.generic.tsv;
{params.command}/phyloseq_import_data.py -b {input.biom_file} -s {input.popmap_file} -t tree.nwk ; {params.command}/phyloseq_import_data.py -b {input.biom_file} -s {input.popmap_file} -t tree.nwk ;
echo \"2\t./{params.stepDir}/phyloseq_import_summary.nb.html\" > {params.outDir}/text.generic.tsv;
{params.command}/phyloseq_composition.py -r phyloseq_data.Rdata -r1 Kingdom -s1 Bacteria -r2 Phylum -n 20 -v {params.varExp} ; {params.command}/phyloseq_composition.py -r phyloseq_data.Rdata -r1 Kingdom -s1 Bacteria -r2 Phylum -n 20 -v {params.varExp} ;
echo \"3\t./{params.stepDir}/phyloseq_composition.nb.html\" > {params.outDir}/text.generic.tsv;
{params.command}/phyloseq_alpha_diversity.py -r phyloseq_data.Rdata -m Observed Chao1 Shannon InvSimpson -v {params.varExp}; {params.command}/phyloseq_alpha_diversity.py -r phyloseq_data.Rdata -m Observed Chao1 Shannon InvSimpson -v {params.varExp};
{params.command}/phyloseq_beta_diversity.py -r phyloseq_data.Rdata -v time -m bray,cc,unifrac,wunifrac --matrix-outdir . ; echo \"4\t./{params.stepDir}/phyloseq_alpha_diversity.nb.html\" > {params.outDir}/text.generic.tsv;
{params.command}/phyloseq_beta_diversity.py -r phyloseq_data.Rdata -v time -m bray,cc,unifrac,wunifrac,jaccard --matrix-outdir . ;
echo \"5\t./{params.stepDir}/phyloseq_beta_diversity.nb.html\" > {params.outDir}/text.generic.tsv;
{params.command}/phyloseq_structure.py -r phyloseq_data.Rdata -v {params.varExp} -d jaccard.tsv; {params.command}/phyloseq_structure.py -r phyloseq_data.Rdata -v {params.varExp} -d jaccard.tsv;
echo \"6\t./{params.stepDir}/phyloseq_structure.nb.html\" > {params.outDir}/text.generic.tsv;
{params.command}/phyloseq_clustering.py -r phyloseq_data.Rdata -v {params.varExp} -d jaccard.tsv; {params.command}/phyloseq_clustering.py -r phyloseq_data.Rdata -v {params.varExp} -d jaccard.tsv;
echo \"7\t./{params.stepDir}/phyloseq_clustering.nb.html\" > {params.outDir}/text.generic.tsv;
{params.command}/phyloseq_manova.py -r phyloseq_data.Rdata -v {params.varExp} -m jaccard.tsv; {params.command}/phyloseq_manova.py -r phyloseq_data.Rdata -v {params.varExp} -m jaccard.tsv;
echo \"8\t./{params.stepDir}/phyloseq_manova.nb.html\" > {params.outDir}/text.generic.tsv;
""" """
\ No newline at end of file
...@@ -7,7 +7,7 @@ ...@@ -7,7 +7,7 @@
description: "Phyloseq to analyse abundance, diversity and structure", description: "Phyloseq to analyse abundance, diversity and structure",
version: "3.2.3", version: "3.2.3",
documentation: "http://frogs.toulouse.inrae.fr/html/commands_utax.html", documentation: "http://frogs.toulouse.inrae.fr/html/commands_utax.html",
multiqc: "custom", multiqc: "generic_iframe",
commands: commands:
[ [
{ {
......
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