diff mothur/README @ 26:5c77423823cb

Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)

--- a/mothur/README	Wed May 16 12:28:44 2012 -0500
+++ b/mothur/README	Wed May 16 13:12:05 2012 -0500
@@ -2,7 +2,7 @@
 
 (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used be mothur commands)
 
-Install mothur v.1.24.1 on your galaxy system so galaxy can execute the mothur command
+Install mothur v.1.25.0 on your galaxy system so galaxy can execute the mothur command
   ( This version of wrappers is designed for Mothur version 1.24 - it may work on later versions )
   http://www.mothur.org/wiki/Download_mothur
   http://www.mothur.org/wiki/Installation
@@ -105,6 +105,10 @@
   tool-data/shared/jars/TreeVector.jar
 
 
+################################################################
+#### If you are manually adding this to your local galaxy:  ####
+################################################################
+
 add config files (*.xml) and wrapper code (*.py) from tools/mothur/*  to your galaxy installation 
 
 
@@ -114,6 +118,7 @@
 import metagenomics # added for metagenomics mothur
 
 
+
 add datatypes to:  datatypes_conf.xml
         <!-- Start Mothur Datatypes -->
         <datatype extension="otu" type="galaxy.datatypes.metagenomics:Otu" display_in_upload="true"/>
@@ -165,19 +170,24 @@
       <tool file="mothur/count.groups.xml"/>
       <tool file="mothur/make.design.xml"/>
       <tool file="mothur/sub.sample.xml"/>
+      <tool file="mothur/sort.seqs.xml"/>
+      <tool file="mothur/create.database.xml"/>
     <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
       <tool file="mothur/sffinfo.xml"/>
       <tool file="mothur/trim.flows.xml"/>
       <tool file="mothur/shhh.flows.xml"/>
+      <tool file="mothur/shhh.seqs.xml"/>
       <tool file="mothur/make.fastq.xml"/>
       <tool file="mothur/fastq.info.xml"/>
       <tool file="mothur/summary.seqs.xml"/>
+      <tool file="mothur/summary.qual.xml"/>
       <tool file="mothur/count.seqs.xml"/>
       <tool file="mothur/reverse.seqs.xml"/>
       <tool file="mothur/list.seqs.xml"/>
       <tool file="mothur/get.seqs.xml"/>
       <tool file="mothur/remove.seqs.xml"/>
       <tool file="mothur/trim.seqs.xml"/>
+      <tool file="mothur/pcr.seqs.xml"/>
       <tool file="mothur/unique.seqs.xml"/>
       <tool file="mothur/deunique.seqs.xml"/>
       <tool file="mothur/chop.seqs.xml"/>
@@ -201,6 +211,7 @@
       <tool file="mothur/chimera.bellerophon.xml"/>
       <tool file="mothur/chimera.ccode.xml"/>
       <tool file="mothur/chimera.check.xml"/>
+      <tool file="mothur/chimera.perseus.xml"/>
       <tool file="mothur/chimera.pintail.xml"/>
       <tool file="mothur/chimera.slayer.xml"/>
       <tool file="mothur/chimera.uchime.xml"/>
@@ -225,6 +236,8 @@
       <tool file="mothur/get.sabund.xml"/>
       <tool file="mothur/get.relabund.xml"/>
       <tool file="mothur/make.shared.xml"/>
+      <tool file="mothur/make.shared_from_biom.xml"/>
+      <tool file="mothur/make.biom.xml"/>
       <tool file="mothur/get.group.xml"/>
       <tool file="mothur/bin.seqs.xml"/>
       <tool file="mothur/get.sharedseqs.xml"/>
@@ -239,8 +252,8 @@
       <tool file="mothur/rarefaction.shared.xml"/>
       <tool file="mothur/normalize.shared.xml"/>
       <tool file="mothur/summary.shared.xml"/>
+      <tool file="mothur/otu.association.xml"/>
       <tool file="mothur/dist.shared.xml"/>
-      <tool file="mothur/heatmap.bin.xml"/>
       <tool file="mothur/heatmap.sim.xml"/>
       <tool file="mothur/venn.xml"/>
       <tool file="mothur/tree.shared.xml"/>
@@ -253,6 +266,7 @@
       <tool file="mothur/homova.xml"/>
       <tool file="mothur/mantel.xml"/>
       <tool file="mothur/anosim.xml"/>
+      <tool file="mothur/cooccurrence.xml"/>
     <label text="Mothur Phylotype Analysis" id="mothur_phylotype_analysis"/>
       <tool file="mothur/get.lineage.xml"/>
       <tool file="mothur/remove.lineage.xml"/>
@@ -261,6 +275,7 @@
       <tool file="mothur/clearcut.xml"/>
       <tool file="mothur/indicator.xml"/>
       <tool file="mothur/deunique.tree.xml"/>
+      <tool file="mothur/classify.tree.xml"/>
       <tool file="mothur/TreeVector.xml"/>
   </section> <!-- metagenomics_mothur -->