comparison mothur/tools/mothur/classify.otu.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

0:3202a38e44d9

<tool id="mothur_classify_otu" name="Classify.otu" version="1.15.0" force_history_refresh="True">
 <description>Assign sequences to taxonomy</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='classify.otu'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy'
  --list=$otu
  --taxonomy=$tax.taxonomy
  #if 100 >= int($cutoff.__str__) > 0:
   --cutoff=$cutoff
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'

   </when>
   <when value="hist">
    <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy Reference"/>
   </when>
  </conditional>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
   </options>
  </param>
  <param name="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100"/>
  <param name="probs" type="boolean" falsevalue="--probs=false" truevalue="" checked="true" label="probs - Show probabilities"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </outputs>

1:fcc0778f6987

<tool id="mothur_classify_otu" name="Classify.otu" version="1.16.0" force_history_refresh="True">
 <description>Assign sequences to taxonomy</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='classify.otu'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy'
  --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
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'

   </when>
   <when value="hist">
    <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy Reference"/>
   </when>
  </conditional>
  <conditional name="reftax">
   <param name="source" type="select" label="Select Taxonomy from" help="">
    <option value="none">None</option>
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>
   <when value="none"/>
   <when value="ref">
    <param name="taxonomy" type="select" format="taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
     <options from_file="mothur_taxonomy.loc">
      <column name="name" index="0" />
      <column name="value" index="1" />
     </options>
    </param>
   </when>
   <when value="hist">
    <param name="taxonomy" type="data" format="taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
   </when>
  </conditional>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
   </options>
  </param>
  <param name="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100">
   <validator type="in_range" message="Confindence percentage cutoff must be between 0 and 100" min="0" max="100"/>
  </param>
  <param name="probs" type="boolean" falsevalue="--probs=false" truevalue="" checked="true" label="probs - Show probabilities"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </outputs>