view summarize_taxa.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="summarize_taxa" name="summarize_taxa" version="1.2.1">
 <description>Summarize Taxa</description>
 <requirements>
  <requirement type="binary">summarize_taxa.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  summarize_taxa.py
  --otu_table_fp=$otu_table_fp
  --output_fp=$output_fp
  --level=$level
  #if $mapping != None and $mapping.__str__ != 'None':
   --mapping=$mapping
  #end if
  #if $delimiter != ';':
   --delimiter=$delimiter
  #end if
  ## --relative_abundance=$relative_abundance
  $absolute_abundance
 </command>
 <inputs>
  <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp"
   help="Path to read otu file [REQUIRED]"/>
  <param name="level" type="integer" value="2" label="level"
   help="Level of taxonomy to use [default: 2]"/>
  <param name="mapping" type="data" format="qiimemapping" optional="true" label="mapping"
   help="if supplied - the taxon information will be added to the mapping file. This mapping file can be used to color PCoA plots by taxon abundance or to perform statistical tests of taxon/mappingy associations."/>
  <param name="delimiter" type="text" value="\;" label="delimiter"
   help="Delimitor that separates taxonomy categories.[default: ;]"/>
  <param name="absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="absolute_abundance"
   help="If present, reports the absolute abundance of the lineage in each sample. By default uses relative abundance [default: False]"/>
 </inputs>
 <outputs>
  <data format="qiimetaxsummary" name="output_fp" label="${tool.name} on ${on_string}: taxa_summary"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>