predict.xml

<tool id="PICRUSt_predict" name="Predict Metagenome" version="1.1.1">
<description></description>

<command interpreter="python" detect_errors="aggressive">

$GALAXY_ROOT_DIR/tools/picrust_galaxy/predict_metagenomes.py -i $inp_data -o $out_file1 -g $gg_version -t $type_of_prediction -a $out_file2

</command>

  <inputs>
	<param format="biom" name="inp_data" type="data" label="Input file"/>

	<param name="gg_version" type="select"  label="GreenGenes Version (used to generate your OTU table)">
		<option value="13_5" selected='True'>GG 13.5</option>
 		<option value="18may2012" >GG 18may2012</option>
	</param>

	<param name="type_of_prediction" type="select"  label="Type of functional predictions">
		<option value="ko" selected='True'>KEGG Orthologs</option>
 		<option value="cog" >COG</option>
		<option value="rfam" >RFAM</option>
	</param>

  </inputs>
  <outputs>
 	<data format="biom" name="out_file1" />
        <data format="txt" name="out_file2" />
  </outputs>
  <help>
Run PICRUSt: Predict Metagenome
--------------------------------------
This module produces a 'virtual' metagenome of KEGG Ortholog abundances for each sample in the given OTU table. A textfile containing accuracy metrics for the predicted metagenome will also be generated (NSTI values). 

**Input file:**
This should be a normalized OTU table populated by the output of the PICRUSt:Normalize by Copy Number module.

For more information please visit:
----------------------------------
http://picrust.github.com/

Citation and Contacts
---------------------
When using PICRUSt please cite: Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Langille, M. G.I.; Zaneveld, J.; Caporaso, J. G.; McDonald, D.; Knights, D.; a Reyes, J.; Clemente, J. C.; Burkepile, D. E.; Vega Thurber, R. L.; Knight, R.; Beiko, R. G.; and Huttenhower, C. Nature Biotechnology, 1-10. 8 2013.

Questions/Comments can be send to:
https://groups.google.com/d/forum/picrust-users

 </help>
</tool>