diff mothur/README @ 7:7bfe1f843858

Support Mothur v1.20 trim.seqs - added name parameter and optional trim.names output phylo.diversity - group optional, put group and groups in conditional - breaks get.lineage remove.lineage - allow multiple taxons dist.shared - added processors consensus.seqs - add cutoff parameter trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs new tools - chimera.uchime deunique.tree count.seqs shared/relabund files - Column headings refactor lib/galaxy/datatypes/metagenomics.py add filters to label and group selects in tool configs mothur_wrapper.py updated with new tools params

--- a/mothur/README	Mon Jun 27 09:34:14 2011 -0500
+++ b/mothur/README	Mon Jun 27 10:12:25 2011 -0500
@@ -1,6 +1,6 @@
 Provides galaxy tools for the Mothur metagenomics package -  http://www.mothur.org/wiki/Main_Page 
 
-Install mothur v.1.19.0 on your galaxy system so galaxy can execute the mothur command
+Install mothur v.1.20.0 on your galaxy system so galaxy can execute the mothur command
   ( This version of wrappers is designed for Mothur version 1.19 - it may work on later versions )
   http://www.mothur.org/wiki/Download_mothur
   http://www.mothur.org/wiki/Installation
@@ -145,6 +145,7 @@
       <tool file="mothur/make.fastq.xml"/>
       <tool file="mothur/fastq.info.xml"/>
       <tool file="mothur/summary.seqs.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"/>
@@ -174,6 +175,7 @@
       <tool file="mothur/chimera.check.xml"/>
       <tool file="mothur/chimera.pintail.xml"/>
       <tool file="mothur/chimera.slayer.xml"/>
+      <tool file="mothur/chimera.uchime.xml"/>
     <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
       <tool file="mothur/pre.cluster.xml"/>
       <tool file="mothur/cluster.fragments.xml"/>
@@ -229,6 +231,7 @@
       <tool file="mothur/phylo.diversity.xml"/>
       <tool file="mothur/clearcut.xml"/>
       <tool file="mothur/indicator.xml"/>
+      <tool file="mothur/deunique.tree.xml"/>
       <tool file="mothur/TreeVector.xml"/>
   </section> <!-- metagenomics_mothur -->
 
@@ -237,8 +240,6 @@
 Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py
 
 * Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
-* Many mothur commands require date to be read into memory (using read.dist, read.otu, read.tree) before executed the command,  
-  these are accomplished in the tool_config and mothur_wrapper.py with --READ_cmd= and --READ_<option> parameters. 
 * Every tool will produce the logfile of the mothur run as an output.
 * When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py
 * When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs 
@@ -264,10 +265,7 @@
  # Each item  conatins:   a regex pattern for matching filenames and  a galaxy datatype (separated by :)
  # The regex match.groups()[0] is used as the id name of the dataset, and must result in  unique name for each output
  --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
- # Many mothur commands first require data to be read into memory using: read.otu, read.dist, or read.tree
- # This prequisite command and its params are prefixed with 'READ_'
- --READ_cmd='read.otu'
- --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat
- --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat'
- --READ_label='unique,0.07'
 
+ ## 
+ ## NOTE:   The "read" commands were eliminated with Mothur version 1.18
+ ##