<tool id="identify_chimeric_seqs" name="identify_chimeric_seqs" version="2.0.0">
 <description>Identify chimeric sequences in input FASTA file</description>
 <requirements>
  <requirement type="binary">identify_chimeric_seqs.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  identify_chimeric_seqs.py
  --input_fasta_fp=$input_fasta_fp
  #if $pick.chimera_detection_method == 'ChimeraSlayer':
    --chimera_detection_method=$pick.chimera_detection_method
    --aligned_reference_seqs_fp=$pick.aligned_reference_seqs_fp
    #if $pick.min_div_ratio.__str__ != '0.0':
    --min_div_ratio=$pick.min_div_ratio
    #end if
  #elif $pick.chimera_detection_method == 'blast_fragments':
    --chimera_detection_method=$pick.chimera_detection_method
    --id_to_taxonomy_fp=$pick.id_to_taxonomy_fp
    #if $pick.blast_db != None and $pick.blast_db.__str__ != "":
    --blast_db=$pick.blast_db
    #else:
    --reference_seqs_fp=$pick.reference_seqs_fp
    #end if
    --num_fragments=$pick.num_fragments
    --taxonomy_depth=$pick.taxonomy_depth
    --max_e_value=$pick.max_e_value
  #end if
  --output_fp=$output_fp
 </command>
 <inputs>
  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
   help="path to the input fasta file (usually result from pick_rep_set) [REQUIRED]"/>
  <conditional name="pick">
   <param name="chimera_detection_method" type="select" label="chimera_detection_method"
    help="Chimera detection method. Choices: blast_fragments or ChimeraSlayer. [default:ChimeraSlayer]">
     <option value="blast_fragments">blast_fragments</option>
     <option value="ChimeraSlayer" selected="true">ChimeraSlayer</option>
   </param>
   <when value="ChimeraSlayer">
    <param name="aligned_reference_seqs_fp" type="data" format="txt" label="aligned_reference_seqs_fp"
     help="Path to (Py)Nast aligned reference sequences. [REQUIRED]"/>
    <param name="min_div_ratio" type="float" value="0.0" label="min_div_ratio"
     help="min divergence ratio (passed to ChimeraSlayer). If set to None uses ChimeraSlayer default value.  [default: None]"/>
   </when>
   <when value="blast_fragments">
    <param name="blast_db" type="text"  label="blast_db"
     help="Database to blast against. Must provide either blast_db or reference_seqs_fp when method is blast_fragments [default: None]"/>
    <param name="reference_seqs_fp" type="data" format="txt" label="reference_seqs_fp"
     help="Path to reference sequences (used to build a blast db when method blast_fragments). [default: None; REQUIRED if no blast_db is provided;]"/>
    <param name="id_to_taxonomy_fp" type="data" format="tabular" label="id_to_taxonomy_fp"
     help="Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a comma-separated list. [REQUIRED]"/>
    <param name="taxonomy_depth" type="integer" value="4" label="taxonomy_depth"
     help="Number of taxonomic divisions to consider when comparing taxonomy assignments [default: 4]"/>
    <param name="num_fragments" type="integer" value="3" label="num_fragments"
     help="Number of fragments to split sequences into (i.e., number of expected breakpoints + 1) [default: 3]"/>
    <param name="max_e_value" type="float" value="1e-30" label="max_e_value"
     help="Max e-value to assign taxonomy [default: 1e-30]"/>
   </when>
  </conditional> <!-- pick -->
 </inputs>
 <outputs>
  <data format="txt" name="output_fp" label="${tool.name} on ${on_string}: chimeras"/>
 </outputs>
 <tests>
 </tests>
 <help>For more information, see identify_chimeric_seqs_ in the Qiime documentation.
 
Updated and validated 01/19/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN

.. _identify_chimeric_seqs: http://qiime.org/scripts/identify_chimeric_seqs.html</help>
</tool>