<tool id="align_seqs" name="align_seqs" version="2.0.0">
 <description>Align sequences using a variety of alignment methods</description>
 <requirements>
  <requirement type="binary">align_seqs.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_outputdir='$log.extra_files_path'
  --galaxy_datasets='^\S+_aligned\.\S+$:'$aligned_fasta,'^\S+_log\.txt$:'$log,'^\S+_failures\.fasta$:'$failures
  align_seqs.py
  --input_fasta_fp=$input_fasta_fp
  --alignment_method=$alignment_method
  #if $alignment_method.__str__ == 'pynast':
    #if $alignment.template_fp != None and $alignment.template_fp.__str__ != 'None' and $alignment.template_fp.__str__ != '':
    --template_fp=$alignment.template_fp
    #end if
    --pairwise_alignment_method=$pairwise_alignment_method
    --min_length=$min_length
    --min_percent_id=$min_percent_id
    #if $blast_db != None and $blast_db.__str__ != 'None' and $blast_db.__str__ != '':
    --blast_db=$blast_db
    #end if
  #elif $alignment_method.__str__ == 'infernal':
    --template_fp=$alignment.template_fp
  #end if

  --output_dir='$log.extra_files_path'
 </command>
 <inputs>
  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp" help="path to the input fasta file (usually output from pick_rep_set) [REQUIRED]"/>
    <param name="alignment_method" type="select" label="alignment_method"
     help="Method for aligning sequences. [default: pynast]">
      <option value="pynast" selected="true">pynast</option>
      <option value="infernal">infernal</option>
      <option value="clustalw">clustalw</option>
      <option value="muscle">muscle</option>
      <option value="mafft">mafft</option>
    </param>
    <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_fp" type="select" label="template - Select an alignment database " help="">
         <options>
          <column name="name" index="0" />
          <column name="value" index="1" />
         </options>
        </param>
       </when>
       <when value="hist">
        <param name="template_fp" type="data" format="txt" label="template_fp" optional="true"
         help="Filepath for template against [REQUIRED ONLY if for alignment_method pynast or infernal]"/>
       </when>
      </conditional> <!--alignment-->
      <param name="pairwise_alignment_method" type="select" label="pairwise_alignment_method"
       help="Method for performing pairwise alignment; only required for PyNAST. [default: uclust]">
        <option value="muscle">muscle</option>
        <option value="pair_hmm">pair_hmm</option>
        <option value="clustal">clustal</option>
        <option value="blast">blast</option>
        <option value="uclust" selected="true">uclust</option>
        <option value="mafft">mafft</option>
      </param>
      <param name="min_length" type="integer" optional="true" value="150" label="min_length"
       help="Minimum sequence length to include in alignment [default: 150]"/>
      <param name="min_percent_id" type="float" value="0.75" optional="true" label="min_percent_id"
       help="Minimum percent sequence identity to closest blast hit to include sequence in alignment [default: 0.75]"/>
      <param name="blast_db" type="data" format="txt"  label="blast_db" optional="true"
       help="Database to blast against when -m pynast [default: created on-the-fly from template_alignment]"/>
      <!-- Template alignment must be in Stockholm format with corresponding secondary structure annotation when using InfernalAligner. -->
    
 </inputs>
 <outputs>
   <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
   <data format="fasta" name="aligned_fasta" label="${tool.name} on ${on_string}: aligned fasta" />
   <data format="fasta" name="failures" label="${tool.name} on ${on_string}: failures" />
 </outputs>
 <tests>
 </tests>
 <help>  .. class:: warningmark
Note: MUSCLE alignment is still not verified. Use at your own risk.
  
For more information, see align_seqs_ in the Qiime documentation.
 
Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA

Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN  

.. _align_seqs: http://qiime.org/scripts/align_seqs.html</help>
</tool>