<tool id="alpha_diversity" name="alpha_diversity" version="1.2.0">
 <description>Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics</description>
 <requirements>
  <requirement type="binary">alpha_diversity.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  #if $run_type.input_type.__str__ == "multi":
  --galaxy_logfile=$output_path
  --galaxy_outputdir=$output_path.extra_files_path
  #end if
  alpha_diversity.py
  #if $run_type.input_type.__str__ == "multi":
  --input_path=$input_path.extra_files_path
  --output_path=$output_path.extra_files_path
  #else:
  --output_path=$output_path
  --input_path=$input_path
  #end if
  --metrics=$metrics
  #if $metrics.__str__ == 'PD_whole_tree':
  --tree_path=$tree_path
  #end if

 </command>
 <inputs>
  <conditional name="run_type">
  <param name="input_type" type="select" label="Input Type" help="Select the type/number of input file(s). If multiple rarefactions have been run, select Multiple File Alpha Diversity.">
   <option value="single">Single File Alpha Diversity</option>
   <option value="multi" selected="true">Multiple File (batch) Alpha Diversity</option>
  </param>
  <when value="single">
    <param name="input_path" type="data"  format="txt"  label="OTU table" help="Rarefied table for single file operation [REQUIRED]"/>
  </when>
  <when value="multi">
    <param name="input_path" type="data" format="txt" label="Multiple Rarefactions Log File" help="multiple_rarefactions log file for multiple file operation. [REQUIRED]"/>
  </when>
  </conditional>
  <param name="metrics" type="select"  multiple="true" label="metrics"
   help="metrics to use">
      <option value="ACE">ACE</option>
      <option value="berger_parker_d">berger_parker_d</option>
      <option value="brillouin_d">brillouin_d</option>
      <option value="chao1">chao1</option>
      <option value="chao1_confidence">chao1_confidence</option>
      <option value="dominance">dominance</option>
      <option value="doubles">doubles</option>
      <option value="equitability">equitability</option>
      <option value="fisher_alpha">fisher_alpha</option>
      <option value="heip_e">heip_e</option>
      <option value="kempton_taylor_q">kempton_taylor_q</option>
      <option value="margalef">margalef</option>
      <option value="mcintosh_d">mcintosh_d</option>
      <option value="mcintosh_e">mcintosh_e</option>
      <option value="menhinick">menhinick</option>
      <option value="michaelis_menten_fit">michaelis_menten_fit</option>
      <option value="observed_species">observed_species</option>
      <option value="osd">osd</option>
      <option value="reciprocal_simpson">reciprocal_simpson</option>
      <option value="robbins">robbins</option>
      <option value="shannon">shannon</option>
      <option value="simpson">simpson</option>
      <option value="simpson_e">simpson_e</option>
      <option value="singles">singles</option>
      <option value="strong">strong</option>
      <option value="PD_whole_tree">PD_whole_tree</option>
  </param>
  <param name="tree_path" type="data"  format="tre"  label="tree_path" optional="true"
   help="path to newick tree file, REQUIRED for phylogenetic metrics: PD_whole_tree"/>
 </inputs>
 <outputs>
  <data format="txt" name="output_path" label="${tool.name} on ${on_string}: alpha_diversity log file"/>
 </outputs>
 <tests>
 </tests>
 <help>This tool calculates alpha diversity, or within-sample diversity, using an otu table. Metrics may be selected in any combination. Input can be the log file from multiple_rarefactions (batch alpha diversity), or a single rarefied OTU table (single_rarefaction/single file alpha diversity). When the phylogenetic metric PD_whole_tree is selected, a .tre file must be supplied for the tool to run. The output file is a log file listing all the alpha rarefaction files produced.
 
For more information, see alpha_diversity_ in the Qiime documentation.
 
Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA

Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN

.. _alpha_diversity: http://qiime.org/scripts/alpha_diversity.html</help>
</tool>