Mercurial > repos > simon-gladman > phyloseq_nmds
changeset 4:d06ddf67468f draft default tip
planemo upload commit 5ca7dbbc2e9d6107b706376cd36742cf0c816534-dirty
| author | simon-gladman |
|---|---|
| date | Tue, 04 Sep 2018 21:41:23 -0400 |
| parents | 5a2bda9b28c5 |
| children | |
| files | README.txt phyloseq_nmds.xml |
| diffstat | 2 files changed, 1 insertions(+), 40 deletions(-) [+] |
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--- a/README.txt Mon Jul 30 21:06:56 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -# 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.
--- a/phyloseq_nmds.xml Mon Jul 30 21:06:56 2018 -0400 +++ b/phyloseq_nmds.xml Tue Sep 04 21:41:23 2018 -0400 @@ -96,7 +96,7 @@ +distance=bray +kingdom=Phylum +cutoff=5 +keep=5 +outdir=outputdir +htmlfile=biom_out.html --> <conditional name="file_source"> <param name="file_source_selector" value="set_biom"/> - <param name="input" value="GP.biom" /> + <param name="input" value="GP.biom" ftype="biom1" /> <param name="subsetColumn" value="Primer" /> </conditional> <output name="htmlfile" ftype="html" file="biom_out.html" />