<tool id="mothur_classify_seqs" name="Classify.seqs" version="1.15.0">
 <description>Assign sequences to taxonomy</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='classify.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.taxonomy$:'$taxonomy_out,'^\S+\.tax\.summary$:'$tax_summary
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --template=$alignment.template
  --taxonomy=$tax.taxonomy
  #if $classify.method == 'bayesian': 
   --method=$classify.method
   #if 15 >= int($classify.ksize.__str__) >= 4:
    --ksize=$classify.ksize
   #end if
   #if int($classify.iters.__str__) > 0:
    --iters=$classify.iters
   #end if
   #if 100 >= int($classify.cutoff.__str__) > 0:
    --cutoff=$classify.cutoff
   #end if
   $classify.probs
  #elif $classify.method == 'knn': 
   --method=$classify.method
   --numwanted=$classify.search.numwanted
   #if $classify.search.algorithm == 'kmer':
    --search=$classify.search.algorithm
    --ksize=$classify.search.ksize
   #elif $classify.search.algorithm == 'blast':
    --search=$classify.search.algorithm
    --match=$classify.search.match
    --mismatch=$classify.search.mismatch
    --gapopen=$classify.search.gapopen
    --gapextend=$classify.search.gapextend
   #elif $classify.knn.search == 'suffix':
    --search=$classify.search.algorithm
   #elif $classify.search.algorithm == 'distance':
    --search=$classify.search.algorithm
   #end if
  #end if
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
  <conditional name="alignment">
   <param name="source" type="select" label="Select Template from" help="">
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>
   <when value="ref">
    <param name="template" type="select" label="template - Select an alignment database " help="">
     <options from_file="mothur_aligndb.loc">
      <column name="name" index="0" />
      <column name="value" index="1" />
     </options>
    </param>
   </when>
   <when value="hist">
    <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/>
   </when>
  </conditional>
  <conditional name="tax">
   <param name="source" type="select" label="Select Taxonomy from" help="">
    <option value="ref">Cached Reference</option>
    <option value="hist">History</option>
   </param>
   <when value="ref">
    <param name="taxonomy" type="select" format="taxonomy" label="taxonomy - Taxonomy reference">
     <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="taxonomy - Taxonomy reference"/>
   </when>
  </conditional>
  <conditional name="classify">
   <param name="method" type="select" label="method - Select a classification method" help="">
    <option value="bayesian">Bayesian (default)</option>
    <option value="knn">K-Nearest Neighbor (knn)</option>
   </param>
   <when value="bayesian">
    <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12"/>
    <param name="iters" type="integer" value="100" label="iters - iterations to do when calculating the bootstrap confidence score"/>
    <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"/>
   </when>
   <when value="knn">
    <param name="numwanted" type="integer" value="10" label="numwanted - "/>
    <conditional name="search">
     <param name="algorithm" type="select" label="algorithm - " help="">
      <option value="kmer">Kmer (default)</option>
      <option value="blast">BLAST</option>
     </param>
     <when value="kmer">
      <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12"/>
     </when>
     <when value="blast">
      <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
      <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
      <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
      <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
     </when>
     <when value="suffix"/>
     <when value="distance"/>
    </conditional>
   </when>
  </conditional>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: taxonomy" />
  <data format="tax.summary" name="tax_summary" label="${tool.name} on ${on_string}: tax.summary" />
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

Mothur_, initiated by Dr. Patrick Schloss and his software development team
in the Department of Microbiology and Immunology at The University of Michigan,
provides bioinformatics for the microbial ecology community.

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The classify.seqs_ command assigns sequences to chosen taxonomy outline.

.. _classify.seqs: http://www.mothur.org/wiki/Classify.seqs


 </help>
</tool>