diff mothur/tools/mothur/deunique.tree.xml @ 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/deunique.tree.xml	Mon Jun 27 10:12:25 2011 -0500
@@ -0,0 +1,42 @@
+<tool id="mothur_deunique_tree" name="Deunique.tree" version="1.20.0">
+ <description>Reinsert the redundant sequence identiers back into a unique tree.</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='deunique.tree'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.deunique\.tre$:'$out_tree
+  --outputdir='$logfile.extra_files_path'
+  --tree=$tree
+  --name=$names
+ </command>
+ <inputs>
+  <param name="tree" type="data" format="tre" label="tree - Sequences to filter"/>
+  <param name="names" type="data" format="names" label="names - Sequences Name reference"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format_source="tree" name="out_tree" label="${tool.name} on ${on_string}: deunique.tre" />
+ </outputs>
+ <requirements>
+  <requirement type="binary">mothur</requirement>
+ </requirements>
+ <tests>
+ </tests>
+ <help>
+**Mothur Overview**
+
+Mothur_, initiated by Dr. Patrick Schloss and his software development team
+in the Department of Microbiology and Immunology at The University of Michigan,
+provides bioinformatics for the microbial ecology community.
+
+.. _Mothur: http://www.mothur.org/wiki/Main_Page
+
+**Command Documenation**
+
+The deunique.tree_ command is the reinserts the redundant sequence identiers back into a unique tree using a name_ file. 
+
+.. _name: http://www.mothur.org/wiki/Name_file
+.. _deunique.tree: http://www.mothur.org/wiki/Deunique.tree
+
+
+ </help>
+</tool>