<tool id="multiple_rarefactions" name="multiple_rarefactions" version="1.2.0">
 <description>Perform multiple subsamplings/rarefactions on an otu table</description>
 <requirements>
  <requirement type="binary">multiple_rarefactions.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_logfile=$output1
  --galaxy_outputdir=$output1.extra_files_path
  multiple_rarefactions.py
  --input_path=$input_path
  --output_path=$output1.extra_files_path
  --min=$min
  --max=$max
  --step=$step
  --num-reps=$num_reps
  $lineages_included
  $keep_empty_otus
 </command>
 <inputs>
  <param name="input_path" type="data"  label="input_path"
   help="Input otu table filepath [REQUIRED]"/>
  <param name="min" type="integer" value="100" label="min"
   help="Min seqs/sample [REQUIRED]"/>
  <param name="max" type="integer" value="400" label="max"
   help="Max seqs/sample (inclusive) [REQUIRED]"/>
  <param name="step" type="integer" value="100" label="step"
   help="Size of each steps between the min/max of seqs/sample (e.g. min, min+step... for every level less than or equal to max). [REQUIRED]"/>
  <param name="num_reps" type="integer" value="10" label="num-reps"
   help="Number of iterations at each seqs/sample level [default: 10]"/>
  <param name="lineages_included" type="boolean" truevalue="--lineages_included" falsevalue="" checked="false" label="lineages_included"
   help="Output rarefied otu tables will include taxonomic (lineage) information for each otu, if present in input otu table [default: False]"/>
  <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus"
   help="otus (rows) of all zeros are usually omitted from the output otu tables, with -k they will not be removed from the output files [default: False]"/>
 </inputs>
 <outputs>
  <data format="txt" name="output1" label="${tool.name} on ${on_string}: Rarefied tables from $min to $max, with a step of $step"/>
 </outputs>
 <tests>
 </tests>
 <help>This tool rarefies OTU tables for use in jackknife, bootstrap, and rarefaction analyses. Samples with fewer sequences than the rarefaction depth requested for a given output otu table are omitted from those otu tables. The input is an OTU table (e.g., the output from make_otu_table). The output file is a log file listing all the rarefied otu tables produced.
 
For more information, see multiple_rarefactions_ 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

.. _multiple_rarefactions: http://qiime.org/scripts/multiple_rarefactions.html</help>
</tool>