diff mothur/tools/mothur/phylo.diversity.xml @ 0:3202a38e44d9

Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/phylo.diversity.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,85 @@
+<tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.15.0">
+ <description>Alpha Diversity calculate unique branch length</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='phylo.diversity'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.phylodiv\.summary$:'$summary_out,'^\S+\.phylodiv$:'$collectors_out,'^\S+\.rarefaction$:'$rarefaction_out
+  --outputdir='$logfile.extra_files_path'
+  --READ_cmd='read.tree'
+  --READ_tree=$tree
+  #if $group.__str__ != "None" and len($group.__str__) > 0:
+   --READ_group='$group'
+  #end if
+  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
+   --groups='$groups'
+  #end if
+  #if int($iters.__str__) > 0:
+   --iters=$iters
+  #end if
+  #if float($freq.__str__) > 0:
+   --freq=$freq
+  #end if
+  $scale
+  $summary
+  $collect
+  $rarefy
+ </command>
+ <inputs>
+  <!-- list,group  or shared -->
+  <param name="tree" type="data" format="tre" label="read.tree(tree=) - Phylogenetic Tree"/>
+  <param name="group" type="data" format="groups" label="read.tree(group=) - Group file for the tree"/>
+  <param name="groups" type="select" label="groups - Groups to display" multiple="true">
+   <options from_dataset="group">
+    <column name="name" index="1"/>
+    <column name="value" index="1"/>
+    <filter type="unique_value" name="unq_grp" column="1" />
+   </options>
+  </param>
+  <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/>
+  <param name="freq" type="float" value="0.0" label="freq - Reporting frequency" 
+         help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/>
+
+  <param name="scale" type="boolean" truevalue="--scale=true" falsevalue="" checked="false" label="scale - Scale output to the number of sequences sampled" />
+  <param name="rarefy" type="boolean" truevalue="--rarefy=true" falsevalue="" checked="false" label="rarefy - Calculate the rarefaction data" />
+  <param name="summary" type="boolean" truevalue="" falsevalue="--summary=false" checked="true" label="summary - Generate a summary file" />
+  <param name="collect" type="boolean" truevalue="--collect=true" falsevalue="" checked="false" label="collect - Create a collectors curve" />
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="tabular" name="summary_out" label="${tool.name} on ${on_string}: summary">
+   <filter>summary == True</filter>
+  </data>
+  <data format="tabular" name="rarefaction_out" label="${tool.name} on ${on_string}: rarefaction">
+   <filter>rarefy == True</filter>
+  </data>
+  <data format="tabular" name="collectors_out" label="${tool.name} on ${on_string}: collectors">
+   <filter>collect == True</filter>
+  </data>
+  <!-- random uses input prompts, not sure how to model that
+  <data format="tabular" name="random" label="${tool.name} on ${on_string}: random">
+  </data>
+  -->
+ </outputs>
+ <requirements>
+  <requirement type="binary">mothur</requirement>
+ </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 phylo.diversity_ command calculates alpha diversity as the total of the unique branch length. 
+
+.. _phylo.diversity: http://www.mothur.org/wiki/Phylo.diversity
+
+
+ </help>
+</tool>