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date Wed, 05 Sep 2018 22:21:43 -0400
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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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6
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7 Requires:
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8
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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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19
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20 ## Version history:
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21
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22 **XML Wrapper:**
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23
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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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28 * Incorporated tests
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29 * Requirements
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30 * Version statement
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31 * Citations
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33 1.22.3.2: Michael Thang QFAB, Simon Gladman Melbourne Bioinformatics
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35 * Uses new version of BIOM1 datatype to get metadata
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36 * Output label changed as per user requirements
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39 **R Script: phyloseq_nmds.R**
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41 0.1.0: Michael Thang QFAB
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43 * Original version
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44
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45 0.1.1: Michael Thang QFAB
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47 * Added extra BIOM import functionality so it doesn't solely rely on phyloseq's internal importer.
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49 0.1.2: Michael Thang QFAB
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51 * BIOM functionality now requires the column header name in text.