view alpha_diversity.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="alpha_diversity" name="alpha_diversity" version="1.2.0">
 <description>Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics</description>
 <requirements>
  <requirement type="binary">alpha_diversity.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  alpha_diversity.py
  --input_path=$input_path
  --output_path=$output_path
  --metrics=$metrics
  #if $tree_path.__str__ != "None" and len($tree_path.__str__) > 0:
    --tree_path=$tree_path
  #end if

 </command>
 <inputs>
  <param name="input_path" type="data"  format="tabular"  label="OTU table"
   help="input path.  directory for batch processing, filename for single file operation"/>
  <param name="metrics" type="select"  multiple="true" label="metrics"
   help="metrics to use">
      <option value="ACE">ACE</option>
      <option value="berger_parker_d">berger_parker_d</option>
      <option value="brillouin_d">brillouin_d</option>
      <option value="chao1">chao1</option>
      <option value="chao1_confidence">chao1_confidence</option>
      <option value="dominance">dominance</option>
      <option value="doubles">doubles</option>
      <option value="equitability">equitability</option>
      <option value="fisher_alpha">fisher_alpha</option>
      <option value="heip_e">heip_e</option>
      <option value="kempton_taylor_q">kempton_taylor_q</option>
      <option value="margalef">margalef</option>
      <option value="mcintosh_d">mcintosh_d</option>
      <option value="mcintosh_e">mcintosh_e</option>
      <option value="menhinick">menhinick</option>
      <option value="michaelis_menten_fit">michaelis_menten_fit</option>
      <option value="observed_species">observed_species</option>
      <option value="osd">osd</option>
      <option value="reciprocal_simpson">reciprocal_simpson</option>
      <option value="robbins">robbins</option>
      <option value="shannon">shannon</option>
      <option value="simpson">simpson</option>
      <option value="simpson_e">simpson_e</option>
      <option value="singles">singles</option>
      <option value="strong">strong</option>
      <option value="PD_whole_tree">PD_whole_tree</option>
  </param>
  <param name="tree_path" type="data"  format="tre"  label="tree_path" optional="true"
   help="path to newick tree file, required for phylogenetic metrics: PD_whole_tree"/>
 </inputs>
 <outputs>
  <data format="tabular" name="output_path" label="${tool.name} on ${on_string}: alpha_diversity"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>