|
3
|
1 # Phloseq_NMDS
|
|
|
2
|
|
|
3 A Galaxy tool to produce NMDS plots using Phyloseq from either a BIOM1 file or 2 input tables.
|
|
|
4
|
|
|
5 Currently produces the plots embedded in a html file for output with links to a PDF file.
|
|
|
6
|
|
|
7 Requires:
|
|
|
8
|
|
|
9 Phyloseq 1.22.3
|
|
|
10 r-getopt 1.20.0
|
|
|
11 ghostscript 9.18
|
|
|
12
|
|
|
13
|
|
|
14 ### Run phyloseq_nmds.R with three input files
|
|
|
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
|
|
|
16
|
|
|
17 ### Run phyloseq_nmds.R with biom file
|
|
|
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
|
|
|
19
|
|
|
20 ## Version history:
|
|
|
21
|
|
|
22 **XML Wrapper:**
|
|
|
23
|
|
|
24 Alpha version by Michael Thang of QFAB, Australia.
|
|
|
25
|
|
|
26 1.22.3.1: Simon Gladman Melbourne Bioinformatics
|
|
|
27
|
|
|
28 * Incorporated tests
|
|
|
29 * Requirements
|
|
|
30 * Version statement
|
|
|
31 * Citations
|
|
|
32
|
|
|
33 1.22.3.2: Michael Thang QFAB, Simon Gladman Melbourne Bioinformatics
|
|
|
34
|
|
|
35 * Uses new version of BIOM1 datatype to get metadata
|
|
|
36 * Output label changed as per user requirements
|
|
|
37
|
|
|
38
|
|
|
39 **R Script: phyloseq_nmds.R**
|
|
|
40
|
|
|
41 0.1.0: Michael Thang QFAB
|
|
|
42
|
|
|
43 * Original version
|
|
|
44
|
|
|
45 0.1.1: Michael Thang QFAB
|
|
|
46
|
|
|
47 * Added extra BIOM import functionality so it doesn't solely rely on phyloseq's internal importer.
|
|
|
48
|
|
|
49 0.1.2: Michael Thang QFAB
|
|
|
50
|
|
|
51 * BIOM functionality now requires the column header name in text.
|
