view single_rarefaction.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="single_rarefaction" name="single_rarefaction" version="1.2.0">
 <description>Perform rarefaction on an otu table</description>
 <requirements>
  <requirement type="binary">single_rarefaction.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  single_rarefaction.py
  --input_path=$input_path
  --output_path=$output_path
  --depth=$depth
  $lineages_included
  $keep_empty_otus
 </command>
 <inputs>
  <param name="input_path" type="qiimeotutable"  label="input_path"
   help="input otu table filepath [REQUIRED]"/>
  <param name="depth" type="integer" value="-1" label="depth"
   help="sequences per sample to subsample [REQUIRED]"/>
  <param name="lineages_included" type="boolean" truevalue="--lineages_included" falsevalue="" checked="false" label="lineages_included"
   help="output rarefied otu tables will include taxonomic (lineage) information for each otu, if present in input otu table [default: False]"/>
  <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus"
   help="otus (rows) of all zeros are usually omitted from the output otu table, with -k they will not be removed from the output file [default: False]"/>
 </inputs>
 <outputs>
  <data format_source="input_path" name="output_path" label="${tool.name} on ${on_string}: rarefaction"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>