# HG changeset patch
# User simon-gladman
# Date 1536111683 14400
# Node ID d06ddf67468f58e4e6ef5e68b3c84365843b4526
# Parent  5a2bda9b28c533be048548a312c72b685da1cb5b
planemo upload commit 5ca7dbbc2e9d6107b706376cd36742cf0c816534-dirty

diff -r 5a2bda9b28c5 -r d06ddf67468f README.txt
--- 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.
diff -r 5a2bda9b28c5 -r d06ddf67468f phyloseq_nmds.xml
--- 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" />