normalize.xml

<tool id="PICRUSt_normalize" name="Normalize by Copy Number" version="1.1.1">
<description></description>

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

$GALAXY_ROOT_DIR/tools/picrust_galaxy/normalize_by_copy_number.py -i $inp_data -o $out_file1 -g $gg_version

</command>
  <inputs>
	<param format="biom" name="inp_data" type="data" label="Input file - Please upload using the standard Galaxy 'Get Data' - Be sure to select file format 'biom' for the 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>

  </inputs>

  <outputs>
    <data format="biom" name="out_file1" />
  </outputs>

  <help>

PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
-----------------------------------------------------------------------------------------
The PICRUSt project aims to support prediction of the unobserved character states in a community of organisms from phylogenetic information about the organisms in that community. The primary application is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.

**First Step**
--------------
Please ensure that you have properly created your OTU table to be compatible with PICRUSt by following this guide: http://picrust.github.com/picrust/methods/constructing_reference_otus.html

Please **upload your OTU file** using the Standard Galaxy Upload Utility. (Get Data / Upload File from your computer)


.. class:: infomark

Please be sure to select file format **biom** for the input file (NOTE: legacy tab-delimited input files are not supported in this instance of PICRUSt. You can convert these files into BIOM format by using "Biom convert").

A **sample file** can be downloaded from: https://raw.github.com/picrust/picrust/master/tutorials/hmp_mock_16S.tab 

**Second Step**
---------------
Run 'Normalize by Copy Number' to correct your OTU table for multiple 16S copy number (this panel).   

**Third Step**
---------------
Run the 'Predict Metagenome' on the output of the previous step (normalized OTU table) to get your metagenome predictions.

Description of PICRUSt: Normalize by Copy Number module
-------------------------------------------------------
This module corrects the abundance of each OTU to better reflect the true organism abundance by normalizing by PICRUSt's prediction of 16S copy number for each OTU.

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>