Mercurial > repos > simon-gladman > phyloseq_nmds

annotate README.txt @ 3:5a2bda9b28c5 draft

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New version 1.22.3.2.
author simon-gladman
date Mon, 30 Jul 2018 21:06:56 -0400
parents 20adf95eb758
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1 # Phloseq_NMDS
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3 A Galaxy tool to produce NMDS plots using Phyloseq from either a BIOM1 file or 2 input tables.
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5 Currently produces the plots embedded in a html file for output with links to a PDF file.
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7 Requires:
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9 Phyloseq 1.22.3
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10 r-getopt 1.20.0
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11 ghostscript 9.18
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14 ## Run phyloseq_nmds.R with three input files
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15 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
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17 ## Run phyloseq_nmds.R with biom file
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18 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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20 Version history:
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22 XML Wrapper:
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24 Alpha version by Michael Thang of QFAB, Australia.
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26 1.22.3.1: Simon Gladman, Melbourne Bioinformatics
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27 * Incorporated tests
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28 * Requirements
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29 * Version statement
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30 * Citations
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33 R Script: phyloseq_nmds.R
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35 0.1.0:
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36 * Original version
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38 0.1.1:
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39 * Added extra BIOM import functionality so it doesn't solely rely on phyloseq's internal importer.