diff mothur/tools/mothur/phylotype.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

--- a/mothur/tools/mothur/phylotype.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/phylotype.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,9 +1,9 @@
-<tool id="mothur_phylotype" name="Phylotype" version="1.16.0">
+<tool id="mothur_phylotype" name="Phylotype" version="1.19.0">
  <description>Assign sequences to OTUs based on taxonomy</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='phylotype'
-  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund,'^\S+\.rabund$:'$rabund,'^\S+\.list$:'$otulist
   --outputdir='$logfile.extra_files_path'
   --taxonomy=$taxonomy
   #if 50 >= int($cutoff.__str__) > 0:
@@ -17,7 +17,7 @@
   #end if
  </command>
  <inputs>
-  <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy"/>
+  <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/>
   <param name="name" type="data" format="names" optional="true" label="name - Names reference file for the taxonomy"/>
   <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true">
    <option value="0">0</option>
@@ -36,8 +36,8 @@
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank)"/>
-  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species)"/>
+  <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
+  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
   <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
  </outputs>
  <requirements>
@@ -56,8 +56,11 @@
 
 **Command Documenation**
 
-The phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a .list, .rabund and .sabund files.
+The phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
 
+.. _list: http://www.mothur.org/wiki/List_file
+.. _rabund: http://www.mothur.org/wiki/Rabund_file
+.. _sabund: http://www.mothur.org/wiki/Sabund_file
 .. _phylotype: http://www.mothur.org/wiki/Phylotype