diff mothur/tools/mothur/classify.otu.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

--- a/mothur/tools/mothur/classify.otu.xml	Mon Jun 27 09:34:14 2011 -0500
+++ b/mothur/tools/mothur/classify.otu.xml	Mon Jun 27 10:12:25 2011 -0500
@@ -1,4 +1,4 @@
-<tool id="mothur_classify_otu" name="Classify.otu" version="1.19.0" force_history_refresh="True">
+<tool id="mothur_classify_otu" name="Classify.otu" version="1.20.0" force_history_refresh="True">
  <description>Assign sequences to taxonomy</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -25,7 +25,7 @@
   $probs
  </command>
  <inputs>
-  <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List "/>
+  <param name="otu" type="data" format="list" label="list - OTU List "/>
   <conditional name="tax">
    <param name="source" type="select" label="Select Taxonomy from" help="">
     <option value="hist">History</option>
@@ -44,8 +44,8 @@
    </when>
   </conditional>
   <conditional name="reftax">
-   <param name="source" type="select" label="Select Taxonomy from" help="">
-    <option value="none">None</option>
+   <param name="source" type="select" label="Select Reference Taxonomy used in Classify.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
+    <option value="none">Selection is Optional</option>
     <option value="hist">History</option>
     <option value="ref">Cached Reference</option>
    </param>