diff mothur/README @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

--- a/mothur/README	Tue Jun 07 17:32:23 2011 -0400
+++ b/mothur/README	Tue Jun 07 17:35:35 2011 -0400
@@ -1,6 +1,6 @@
 Provides galaxy tools for the Mothur metagenomics package -  http://www.mothur.org/wiki/Main_Page 
 
-Install mothur v.1.15.0 on your galaxy system so galaxy can execute the mothur command
+Install mothur v.1.16.0 on your galaxy system so galaxy can execute the mothur command
   http://www.mothur.org/wiki/Download_mothur
   http://www.mothur.org/wiki/Installation
   ( This Galaxy iMothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )
@@ -132,7 +132,12 @@
       <tool file="mothur/make.group.xml"/>
       <tool file="mothur/get.groups.xml"/>
       <tool file="mothur/remove.groups.xml"/>
+      <tool file="mothur/merge.groups.xml"/>
+      <tool file="mothur/make.design.xml"/>
+      <tool file="mothur/sub.sample.xml"/>
     <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
+      <tool file="mothur/sffinfo.xml"/>
+      <tool file="mothur/fastq.info.xml"/>
       <tool file="mothur/summary.seqs.xml"/>
       <tool file="mothur/reverse.seqs.xml"/>
       <tool file="mothur/list.seqs.xml"/>
@@ -146,38 +151,40 @@
       <tool file="mothur/filter.seqs.xml"/>
       <tool file="mothur/degap.seqs.xml"/>
       <tool file="mothur/consensus.seqs.xml"/>
-      <tool file="mothur/sub.sample.xml"/>
+      <tool file="mothur/align.seqs.xml"/>
+      <tool file="mothur/align.check.xml"/>
+      <tool file="mothur/dist.seqs.xml"/>
+      <tool file="mothur/pairwise.seqs.xml"/>
+      <tool file="mothur/split.abund.xml"/>
+      <tool file="mothur/split.groups.xml"/>
+      <tool file="mothur/pcoa.xml"/>
+      <tool file="mothur/pca.xml"/>
+      <tool file="mothur/nmds.xml"/>
+      <tool file="mothur/corr.axes.xml"/>
+      <tool file="mothur/classify.seqs.xml"/>
+   <label text="Mothur Sequence Chimera Detection" id="mothur_sequence_chimera"/>
       <tool file="mothur/chimera.bellerophon.xml"/>
       <tool file="mothur/chimera.ccode.xml"/>
       <tool file="mothur/chimera.check.xml"/>
       <tool file="mothur/chimera.pintail.xml"/>
       <tool file="mothur/chimera.slayer.xml"/>
-      <tool file="mothur/align.seqs.xml"/>
-      <tool file="mothur/align.check.xml"/>
-      <tool file="mothur/split.abund.xml"/>
-      <tool file="mothur/split.groups.xml"/>
-      <tool file="mothur/parse.list.xml"/>
+    <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
       <tool file="mothur/pre.cluster.xml"/>
       <tool file="mothur/cluster.fragments.xml"/>
-      <tool file="mothur/dist.seqs.xml"/>
-      <tool file="mothur/pairwise.seqs.xml"/>
-      <tool file="mothur/bin.seqs.xml"/>
-      <tool file="mothur/classify.seqs.xml"/>
-      <tool file="mothur/sffinfo.xml"/>
-      <tool file="mothur/fastq.info.xml"/>
-      <tool file="mothur/pcoa.xml"/>
-      <tool file="mothur/get.lineage.xml"/>
-      <tool file="mothur/remove.lineage.xml"/>
-    <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
       <tool file="mothur/cluster.xml"/>
       <tool file="mothur/hcluster.xml"/>
       <tool file="mothur/cluster.classic.xml"/>
+      <tool file="mothur/cluster.split.xml"/>
+      <tool file="mothur/metastats.xml"/>
       <tool file="mothur/read.otu.xml"/>
       <tool file="mothur/classify.otu.xml"/>
+      <tool file="mothur/parse.list.xml"/>
       <tool file="mothur/get.otus.xml"/>
       <tool file="mothur/remove.otus.xml"/>
+      <tool file="mothur/remove.rare.xml"/>
       <tool file="mothur/get.oturep.xml"/>
       <tool file="mothur/get.relabund.xml"/>
+      <tool file="mothur/get.group.xml"/>
     <label text="Mothur Single Sample Analysis" id="mothur_single_sample_analysis"/>
       <tool file="mothur/collect.single.xml"/>
       <tool file="mothur/rarefaction.single.xml"/>
@@ -199,6 +206,8 @@
       <tool file="mothur/unifrac.unweighted.xml"/>
       <tool file="mothur/libshuff.xml"/>
     <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
+      <tool file="mothur/get.lineage.xml"/>
+      <tool file="mothur/remove.lineage.xml"/>
       <tool file="mothur/phylotype.xml"/>
       <tool file="mothur/phylo.diversity.xml"/>
       <tool file="mothur/clearcut.xml"/>