Mercurial > repos > simon-gladman > phyloseq_nmds

diff README.txt @ 0:b4606394e7ec draft

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planemo upload
author simon-gladman
date Thu, 14 Jun 2018 09:08:23 -0400
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children 20adf95eb758
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+++ b/README.txt	Thu Jun 14 09:08:23 2018 -0400
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+## Run phyloseq_nmds.R with three input files
+Rscript phyloseq_nmds.R --otu_table=GP_OTU_TABLE.txt --tax_table=GP_TAX_TABLE.txt --meta_table=GP_SAMPLE_TABLE.txt --method="bray" --kingdom=2 --cutoff=5 --category=6 --outdir=/outputdir --htmlfile=test.html
+
+## Run phyloseq_nmds.R with biom file
+Rscript phyloseq_nmds.R --biom=GP.biom --subset=6 --method=NMDS --distance=bray --kingdom=Phylum --cutoff=5 --keep=5 --outdir=/outputdir --htmlfile=biom_out.html
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