<tool id="mothur_indicator" name="Indicator" version="1.15.0">
 <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='$logfile.extra_files_path'
  --tree=$tree
  #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=$groups
  #end if
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.indicator.tre$:'$tree_out,'^\S+\.indicator.summary$:'$summary
 </command>
 <inputs>
  <param name="tree" type="data" format="tree" label="tree - A newick-formatted tree"/>
  <param name="otu" type="data" format="shared,relabund" label="shared/relabund - Otu dataset"/>
  <param name="label" type="select" optional="true" label="label - OTU Labels" >
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
    <filter type="unique_value" name="unq_lbl" column="0" />
   </options>
  </param>
  <param name="groups" type="select" optional="true" label="groups - Pick groups to annalyze" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="unique_value" name="unq_grp" column="1" />
   </options>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tre" name="tree_out" label="${tool.name} on ${on_string}: indicator.tre"/>
  <data format="txt" name="summary" label="${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.tre and .indicator.summary file. 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. The summary file lists the indicator value for each OTU for each node.

.. _indicator: http://www.mothur.org/wiki/Indicator


 </help>
</tool>