diff README.txt @ 2:20adf95eb758 draft

Updated phyloseq_nmds.xml to allow for new datatype.

--- a/README.txt	Sat Jun 16 05:03:43 2018 -0400
+++ b/README.txt	Fri Jul 20 00:23:53 2018 -0400
@@ -1,5 +1,39 @@
+# 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
\ No newline at end of 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.