<tool id="pick_reference_otus_through_otu_table" name="pick_reference_otus_through_otu_table" version="1.2.1">
 <description>Reference OTU picking/Shotgun UniFrac workflow.</description>
 <requirements>
  <requirement type="binary">pick_reference_otus_through_otu_table.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  pick_reference_otus_through_otu_table.py
  --input_fp=$input_fp
  --reference_fp=$reference_fp
  --output_dir=$__new_file_path__
  #if $parameter.source == 'hist':
   --parameter_fp=$parameter_fp
  #else:
   --parameter_fp=$parameter_generated
  #end if
  --taxonomy_fp=$taxonomy_fp
  $force
  $print_only
  $parallel
 </command>
 <inputs>
  <param name="input_fp" type="data" format="txt" label="input_fp"
   help="the input sequences [REQUIRED]"/>
  <param name="reference_fp" type="data" format="txt" label="reference_fp"
   help="the reference sequences [REQUIRED]"/>

  <conditional name="parameter">
   <param name="source" type="select" label="Parameters from" help="">
    <option value="hist">Your History</option>
    <option value="build">Build a Parameter file</option>
   </param>
   <when value="hist">
    <param name="parameter_fp" type="data" format="qiimeparams" label="parameter_fp"
     help="path to the parameter file [REQUIRED]"/>
   </when> <!-- hist -->
   <when value="build">
   <!--
        params['alpha_diversity']['metrics'].split(',')
        params['multiple_rarefactions']
        params['parallel'])
        params['alpha_diversity'])
        params['collate_alpha']
        params['make_rarefaction_plots']
    multiple_rarefactions.py
     min seqs/sample
     max seqs/sample
     step
     depth    sequences per sample to subsample
     num-reps
     lineages_included 
     keep_empty_otus
    alpha_diversity.py
    collate_alpha.py
    make_rarefaction_plots.py
   -->
   </when> <!-- build -->
  </conditional> <!-- parameter -->

  <param name="taxonomy_fp" type="data" format="tabular" label="taxonomy_fp"
   help="the taxonomy map [default: ('NO', 'DEFAULT')]"/>
  <param name="force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="force"
   help="Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: ('NO', 'DEFAULT')]"/>
  <param name="print_only" type="boolean" truevalue="--print_only" falsevalue="" checked="false" label="print_only"
   help="Print the commands but don't call them -- useful for debugging [default: False]"/>
  <param name="parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="parallel"
   help="Run in parallel where available [default: False]"/>
 </inputs>
 <configfiles>
  <configfile name="parameter_generated">
alpha_diversity:metrics chao1,observed_species,PD_whole_tree
multiple_rarefactions_even_depth:num-reps       20
parallel:jobs_to_start  2
parallel:retain_temp_files      False
parallel:seconds_to_sleep       60
collate_alpha:example_path
make_rarefaction_plots:imagetype        png
make_rarefaction_plots:resolution       75
make_rarefaction_plots:background_color white
make_rarefaction_plots:prefs_path
  </configfile>
 </configfiles>

 <outputs>
  
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>