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+# Phloseq Ordination Plot
+
+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
+r-doparallel 1.0.11
+ghostscript 9.18
+
+
+### Run phyloseq_ordination_plot.R with three input files
+Rscript 'phyloseq_ordination_plot.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_ordinate_plot.R' --biom='GP.biom' --subset='Primer' --method='NMDS' --distance='bray' --kingdom='Phylum' --plottype='2' --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
+
+1.22.3.2: Michael Thang QFAB, Simon Gladman Melbourne Bioinformatics
+
+* Uses new version of BIOM1 datatype to get metadata
+* Output label changed as per user requirements
+
+
+**R Script: phyloseq_nmds.R**
+
+0.1.0: Michael Thang QFAB
+
+* Original version
+
+0.1.1: Michael Thang QFAB
+
+* Added extra BIOM import functionality so it doesn't solely rely on phyloseq's internal importer.
+
+0.1.2: Michael Thang QFAB
+
+* BIOM functionality now requires the column header name in text.