view README.txt @ 3:5a2bda9b28c5 draft

New version 1.22.3.2.

# Phloseq_NMDS

A Galaxy tool to produce NMDS plots using Phyloseq from either a BIOM1 file or 2 input tables.

Currently produces the plots embedded in a html file for output with links to a PDF file.

Requires:

Phyloseq 1.22.3
r-getopt 1.20.0
ghostscript 9.18


## 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

Version history:

XML Wrapper:

Alpha version by Michael Thang of QFAB, Australia.

1.22.3.1: Simon Gladman, Melbourne Bioinformatics
    * Incorporated tests
    * Requirements
    * Version statement
    * Citations


R Script: phyloseq_nmds.R

0.1.0:
    * Original version

0.1.1:
    * Added extra BIOM import functionality so it doesn't solely rely on phyloseq's internal importer.