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

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

--- a/mothur/tools/mothur/parsimony.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/parsimony.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,36 +1,37 @@
-<tool id="mothur_parsimony" name="Parsimony" version="1.16.0">
+<tool id="mothur_parsimony" name="Parsimony" version="1.19.0">
  <description>Describes whether two or more communities have the same structure</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='parsimony'
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.psummary$:'$psummary,'^\S+\.parsimony$:'$parsimony
   --outputdir='$logfile.extra_files_path'
-  --READ_cmd='read.tree'
-  --READ_tree=$tree
+  --tree=$tree
   #if $group.__str__ != "None" and len($group.__str__) > 0:
-   --READ_group='$group'
+   --group='$group'
   #end if
   #if $groups.__str__ != "None" and len($groups.__str__) > 0:
    --groups='$groups'
   #end if
+  #if $name.__str__ != "None" and len($name.__str__) > 0:
+   --name='$name'
+  #end if
   #if int($iters.__str__) > 0:
    --iters=$iters
   #end if
   --processors=2
  </command>
  <inputs>
-  <param name="tree" type="data" format="tre" label="read.tree(tree=) - Phylogenetic Tree"/>
-  <param name="group" type="data" format="groups" label="read.tree(group=) - Group file for the tree"/>
-  <!--
-  <param name="name" type="data" format="names" optional="true" label="read.tree(name=) - Sequences Name reference file for the tree"/>
-  -->
-  <param name="groups" type="select" label="groups - Groups to display" multiple="true">
+  <param name="tree" type="data" format="tre" label="tree - Phylogenetic Tree"/>
+  <param name="group" type="data" format="groups" label="group - Group file for the tree"/>
+  <param name="groups" type="select" label="groups - Groups to display" multiple="true" 
+         help="By default all are included if no selection is made.">
    <options from_dataset="group">
     <column name="name" index="1"/>
     <column name="value" index="1"/>
     <filter type="unique_value" name="unq_grp" column="1" />
    </options>
   </param>
+  <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file for the tree"/>
   <param name="iters" type="integer" value="1000" label="iters - Number of bootstrap iterations to try (default 1000)"/>
   <!-- random uses input prompts, not sure how to model that
   <param name="random" type="text" value="" label="random - The root name for random tests"/>