<tool id="collate_alpha" name="collate_alpha" version="1.2.0">
 <description>Collate alpha diversity results</description>
 <requirements>
  <requirement type="binary">collate_alpha.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_outputdir=$output1.extra_files_path
  --galaxy_new_files_path='$__new_file_path__'
  --galaxy_logfile=$output1
  --galaxy_new_datasets='^\S+\.txt$:txt'
  --galaxy_datasetid=$output1.id
  collate_alpha.py
  --input_path=$input_path.extra_files_path
  --output_path='$__new_file_path__'
 </command>
 <inputs>
  <param name="input_path" type="data" format="txt"  label="input_path"
   help="Input is alpha diversity log file [REQUIRED]"/>
  <!--<param name="example_path" type="text"  label="example_path"
   help="example alpha_diversity analysis file, containing all samples and all metrics to be included in the collated result[Default: chosen automatically (see usage string)]"/>-->
 </inputs>
 <outputs>
  <data format="txt" name="output1" label="${tool.name} on ${on_string}"/>
 </outputs>
 <tests>
 </tests>
 <help>This tool concatenates all the files generated by alpha_diversity in order to generate rarefaction curves. The input is therefore the log file generated by alpha_diversity, and the output is a log file listing all the output files, as well as the files themselves. Galaxy must be manually refreshed after running this tool to view all output files.
 
For more information, see collate_alpha_ 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

.. _collate_alpha: http://qiime.org/scripts/collate_alpha.html</help>
</tool>