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metagenome.xml
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metagenome.xml
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<tool id="PICRUSt_metagenome" name="Metagenome Contributions" version="1.1.1">
<description></description>
<command interpreter="python" detect_errors="aggressive">
$GALAXY_ROOT_DIR/tools/picrust_galaxy/metagenome_contributions.py -i $inp_data -o $out_file1 -t $type_of_prediction -g $gg_version -l $limit
</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. This should be the output of the Normalize by Copy Number command."/>
<param name="gg_version" type="select" optional="true" 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="limit" format="txt" type="text" label="Limit to specified function ids (required in galaxy version). If limiting to multiple ids then separate them by commas with no spaces between them."/>
<param name="type_of_prediction" type="select" optional="true" 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="txt" 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.
Description of PICRUSt: Metagenome Contributions module
-------------------------------------------------------
This module will output the breakdown of which OTUs are contributing to the abundance of functions in each sample.
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>