comparison mothur/tools/mothur/classify.otu.xml @ 9:9181ff21b48a

Add name param to classify.otu

8:3249eb52a9c1

  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy','^\S+?\.(unique|[0-9.]*\.cons\.tax\.summary)$:tax.summary'
  --list=$otu
  --taxonomy=$tax.taxonomy
  #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0:
   --reftaxonomy=$reftax.taxonomy
  #end if
  #if 100 >= int($cutoff.__str__) > 0:
   --cutoff=$cutoff

  --basis=$basis
  $probs
 </command>
 <inputs>
  <param name="otu" type="data" format="list" label="list - OTU List "/>
  <conditional name="tax">
   <param name="source" type="select" label="Select Taxonomy from" help="">
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>

9:9181ff21b48a

  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy','^\S+?\.(unique|[0-9.]*\.cons\.tax\.summary)$:tax.summary'
  --list=$otu
  --taxonomy=$tax.taxonomy
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name='$name'
  #end if
  #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0:
   --reftaxonomy=$reftax.taxonomy
  #end if
  #if 100 >= int($cutoff.__str__) > 0:
   --cutoff=$cutoff

  --basis=$basis
  $probs
 </command>
 <inputs>
  <param name="otu" type="data" format="list" label="list - OTU List "/>
  <param name="name" type="data" format="names" optional="true" label="name - taxonomy sequence names"/>
  <conditional name="tax">
   <param name="source" type="select" label="Select Taxonomy from" help="">
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>