<tool id="mothur_indicator" name="Indicator" version="1.21.0">
 <description>Identify indicator "species" for nodes on a tree</description>
 <command interpreter="python">
  mothur_wrapper.py 
  ## output {group_file_name}.pick.{label}.groups   {list_file_name}.pick.{label}.list 
  #import re, os.path
  --cmd='indicator'
  --outputdir='$logfile.extra_files_path'
  #if $tree.__str__ != "None" and len($tree.__str__) > 0:
   --tree=$tree
  #end if
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__):
  --relabund=$otu
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label=$label
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups=$groups
  #end if
  #if $design.__str__ != "None" and len($design.__str__) > 0:
   --design=$design
  #end if
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.indicator.tre$:'$tree_out,'^\S+\.indicator.summary$:'$summary
  --processors=8
 </command>
 <inputs>
  <param name="otu" type="data" format="shared,relabund" label="shared/relabund - Otu dataset"/>
  <param name="label" type="select" optional="true" label="label - OTU Labels" >
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
  <param name="groups" type="select" optional="true" label="groups - Pick groups to annalyze" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="groups" />
   </options>
  </param>
  <param name="tree" type="data" format="tree"  optional="true" label="tree - A newick-formatted tree" 
         help="Optional, if a design file is provided."/>
  <param name="design" type="data" format="tabular" optional="true" label="design - assign groups to new grouping"
         help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tre" name="tree_out" label="${tool.name} on ${on_string}: indicator.tre">
   <filter>tree != None</filter>
  </data>
  <data format="tabular" name="summary" label="${tool.name} on ${on_string}: indicator.summary"/>
 </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 indicator_ command reads a shared_ or relabund_ file and a tree file, and outputs a .indicator.summary file and when a tree file is given a .indicator.tre file. The summary file lists the indicator value for each OTU for each node.  The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file. 

.. _shared: http://www.mothur.org/wiki/Shared_file
.. _relabund: http://www.mothur.org/wiki/Get.relabund
.. _indicator: http://www.mothur.org/wiki/Indicator


 </help>
</tool>