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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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<tool id="alpha_rarefaction" name="alpha_rarefaction" version="1.2.0">
 <description>A workflow script for performing alpha rarefaction</description>
 <requirements>
  <requirement type="binary">alpha_rarefaction.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_summary_html='$output_html'
  --galaxy_outputdir='$output_html.extra_files_path'
  --galaxy_summary_template='$output_template'
  ## --galaxy_datasets='^rarefaction_plots.html$:'$output_html
  alpha_rarefaction.py
  --otu_table_fp=$otu_table_fp
  --mapping_fp=$mapping_fp
  --output_dir=$output_html.extra_files_path
  #if $parameter.source == 'hist':
   --parameter_fp=$parameter_fp
  #else:
   --parameter_fp=$parameter_generated
  #end if
  --num_steps=$num_steps
  $force
  $print_only
  $parallel
  #if $tree_fp != None and $tree_fp.__str__ != 'None':
   --tree_fp=$tree_fp
  #end if
 </command>
 <inputs>
  <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp"
   help="the input otu table [REQUIRED]"/>
  <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp"
   help="path to the mapping file [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="num_steps" type="integer" value="10" label="num_steps"
   help="number of steps (or rarefied OTU table sizes) to make between min and max counts [default: 10]"/>
  <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]"/>
  <param name="tree_fp" type="data" format="txt" optional="true" label="tree_fp"
   help="path to the tree file [default: REQUIRED for phylogenetic measures]"/>
 </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>
  <configfile name="output_template">
<![CDATA[
<html>
<body>
<a href="rarefaction_plots.html">rarefaction_plots.html</a>
</body>
</html>
]]>
  </configfile>
 </configfiles>
 <outputs>
  <data format="html" name="output_html" label="alpha_rarefaction_plots"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>