diff mothur/tools/mothur/unifrac.unweighted.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/unifrac.unweighted.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/unifrac.unweighted.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,20 +1,19 @@
-<tool id="mothur_unifrac_unweighted" name="unifrac.unweighted" version="1.16.0">
+<tool id="mothur_unifrac_unweighted" name="unifrac.unweighted" version="1.19.0">
  <description>Describes whether two or more communities have the same structure</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='unifrac.unweighted'
-  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.uwsummary$:'$summary,'^\S+\.unweighted\.(column\.|philip\.)?dist$:'$dist
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.uwsummary$:'$summary,'^\S+\.unweighted\.(column\.|phylip\.)?dist$:'$dist,'^\S+\.unweighted$:'$unweighted
   --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:
-   --READ_name='$name'
+   --name='$name'
   #end if
   #if int($iters.__str__) > 0:
    --iters=$iters
@@ -23,13 +22,15 @@
   #if $distance.__str__ != "false":
    --distance=$distance
   #end if
+  $root
   --processors=2
  </command>
  <inputs>
   <!-- list,group  or shared -->
-  <param name="tree" type="data" format="tre" label="read.tree(tree=) - Tree"/>
-  <param name="group" type="data" format="groups" label="read.tree(group=) - Group 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 - Tree"/>
+  <param name="group" type="data" format="groups" label="group - Group file for the tree"/>
+  <param name="groups" type="select" label="groups - Select groups for pairwise comparisons" multiple="true">
+   <help></help>
    <options from_dataset="group">
     <column name="name" index="1"/>
     <column name="value" index="1"/>
@@ -39,20 +40,21 @@
   <param name="name" type="data" format="names" optional="true" label="name - Names file for the tree"/>
   <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/>
   <param name="random" type="boolean" truevalue="--random=true" falsevalue="" checked="false" label="random - Compare your trees with randomly generated trees" />
-  <param name="distance" type="select" label="distance - Select a distance matrix for your history">
+  <param name="distance" type="select" label="distance - Create a distance matrix for your history">
    <option value="false">None</option>
-   <option value="lt">Philip Lower Triangle Matrix</option>
-   <option value="square">Philip Square Matrix</option>
+   <option value="lt">Phylip Lower Triangle Matrix</option>
+   <option value="square">Phylip Square Matrix</option>
    <option value="column">Pairwise Distance Matrix</option>
   </param>
-  <!-- random uses input prompts, not sure how to model that
-  <param name="random" type="text" value="" label="random - The root name for random tests"/>
-  -->
+  <param name="root" type="boolean" truevalue="--root=true" falsevalue="" checked="false" label="root - the entire root in your calculations" />
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary">
   </data>
+  <data format="tabular" name="unweighted" label="${tool.name} on ${on_string}: unweighted">
+   <filter>(random == True)</filter>
+  </data>
   <data format="lower.dist" name="dist" label="${tool.name} on ${on_string}: dist">
    <filter>distance != 'false'</filter>
    <change_format>
@@ -60,10 +62,6 @@
     <when input="distance" value="column" format="pair.dist" />
    </change_format>
   </data>
-  <!-- random uses input prompts, not sure how to model that
-  <data format="tabular" name="random" label="${tool.name} on ${on_string}: random">
-  </data>
-  -->
  </outputs>
  <requirements>
   <requirement type="binary">mothur</requirement>