Commit e5d78b66 authored by khalid's avatar khalid
Browse files

Append different html output

parent 7d3667f5
......@@ -37,7 +37,7 @@ rule <step_name>__FROGS_affiliation:
--java-mem 20;
echo \"1\t./{params.stepDir}/affi_report.html\" > {params.outDir}/text.generic.tsv
{params.cmdStat} -i {output.abundance_file} --tax-consensus-tag 'blast_taxonomy' --multiple-tag 'blast_affiliations' ;
echo \"2\t./{params.stepDir}/affiliations_stat.html\" > {params.outDir}/text.generic.tsv
echo \"2\t./{params.stepDir}/affiliations_stat.html\" >> {params.outDir}/text.generic.tsv
"""
# {params.rdp} \
#{params.taxonomic_ranks} \
\ No newline at end of file
......@@ -17,25 +17,25 @@ rule <step_name>__FROGS_phyloseq_stats:
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 ;
echo \"2\t./{params.stepDir}/phyloseq_import_summary.nb.html\" > {params.outDir}/text.generic.tsv;
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} ;
echo \"3\t./{params.stepDir}/phyloseq_composition.nb.html\" > {params.outDir}/text.generic.tsv;
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};
echo \"4\t./{params.stepDir}/phyloseq_alpha_diversity.nb.html\" > {params.outDir}/text.generic.tsv;
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;
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;
echo \"6\t./{params.stepDir}/phyloseq_structure.nb.html\" > {params.outDir}/text.generic.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;
echo \"7\t./{params.stepDir}/phyloseq_clustering.nb.html\" > {params.outDir}/text.generic.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;
echo \"8\t./{params.stepDir}/phyloseq_manova.nb.html\" > {params.outDir}/text.generic.tsv;
echo \"8\t./{params.stepDir}/phyloseq_manova.nb.html\" >> {params.outDir}/text.generic.tsv;
"""
\ No newline at end of file
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