<tool id="align_seqs" name="align_seqs" version="1.2.0">
 <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=$align.alignment_method
  #if $align.alignment_method == 'pynast':
    --template_fp=$align.alignment.template_fp
    --pairwise_alignment_method=$align.pairwise_alignment_method
    --min_length=$align.min_length
    --min_percent_id=$align.min_percent_id
    --blast_db=$align.blast_db
  #elif $align.alignment_method == 'infernal':
    --template_fp=$align.alignment.template_fp
  #elif $align.alignment_method == 'clustalw':
    #echo ''
  #elif $align.alignment_method == 'muscle':
    #echo ''
  #elif $align.alignment_method == 'mafft':
    #echo ''
  #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 [REQUIRED]"/>

  <conditional name="align">
    <param name="alignment_method" type="select" label="alignment_method"
     help="Method for aligning sequences. Valid choices are: pynast, infernal, clustalw, muscle, infernal, mafft [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>
  
    <when value="pynast">
      <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 from_file="mothur_aligndb.loc">
          <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"
         help="Filepath for template against [REQUIRED if for alignment_method  pynast or infernal]"/>
       </when>
      </conditional>
      <param name="pairwise_alignment_method" type="select" label="pairwise_alignment_method"
       help="method for performing pairwise alignment in PyNAST. Valid choices are muscle, pair_hmm, clustal, blast, uclust, mafft [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" 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" 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="text"  label="blast_db" optional="true"
       help="Database to blast against when -m pynast [default: created on-the-fly from template_alignment]"/>
    </when> <!-- pynast -->
  
    <when value="infernal">
       <!-- Template alignment must be in Stockholm format with corresponding secondary structure annotation when using InfernalAligner. -->
      <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 from_file="mothur_aligndb.loc">
          <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"
         help="Filepath for template against [REQUIRED if for alignment_method  pynast or infernal]"/>
       </when>
      </conditional>
    </when> <!-- infernal -->

    <when value="clustalw">
    </when> <!-- clustalw -->
    <when value="muscle">
    </when> <!-- muscle -->
    <when value="mafft">
    </when> <!-- mafft -->
  
  </conditional> <!-- align -->


 </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" >
    <filter>align['alignment_method'] == 'pynast'</filter>
   </data>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>