<tool id="parallel_align_seqs_pynast" name="parallel_align_seqs_pynast" version="1.2.0">
 <description>Parallel sequence alignment using PyNAST</description>
 <requirements>
  <requirement type="binary">parallel_align_seqs_pynast.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  parallel_align_seqs_pynast.py
  --input_fasta_fp=$input_fasta_fp
  --output_dir=$__new_file_path__
  --template_fp=$template_fp
  --pairwise_alignment_method=$pairwise_alignment_method
  --blast_db=$blast_db
  --min_length=$min_length
  --min_percent_id=$min_percent_id
  --align_seqs_fp=$align_seqs_fp
  --jobs_to_start=$jobs_to_start
  --poller_fp=$poller_fp
  $retain_temp_files
  $suppress_submit_jobs
  $poll_directly
  --cluster_jobs_fp=$cluster_jobs_fp
  $suppress_polling
  --job_prefix=$job_prefix
  --python_exe_fp=$python_exe_fp
  --seconds_to_sleep=$seconds_to_sleep
 </command>
 <inputs>
  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
   help="path to the input fasta file [REQUIRED]"/>
  <param name="template_fp" type="data" format="txt" label="template_fp"
   help="Filepath for template against [REQUIRED]"/>
  <param name="pairwise_alignment_method" type="select" label="pairwise_alignment_method"
   help="Method to use for pairwise alignments [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="blast_db" type="text"  label="blast_db"
   help="Database to blast against [default: created on-the-fly from template_alignment]"/>
  <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="75.0" label="min_percent_id"
   help="Minimum percent sequence identity to closest blast hit to include sequence in alignment [default: 75.0]"/>
  <param name="align_seqs_fp" type="data" format="txt" label="align_seqs_fp"
   help="full path to Qiime/scripts/align_seqs.py [default: /usr/local/lib/python2.6/site-packages/scripts/align_seqs.py]"/>
  <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start"
   help="Number of jobs to start [default: 1]"/>
  <param name="poller_fp" type="data" format="txt" label="poller_fp"
   help="full path to qiime/parallel/poller.py [default: /usr/local/lib/python2.6/site-packages/scripts/poller.py]"/>
  <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files"
   help="retain temporary files after runs complete (useful for debugging) [default: False]"/>
  <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs"
   help="Only split input and write commands file - don't submit jobs [default: False]"/>
  <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly"
   help="Poll directly for job completion rather than running poller as a separate job. If -T is specified this script will not return until all jobs have completed. [default: False]"/>
  <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp"
   help="path to cluster_jobs.py script  [default: /usr/local/lib/python2.6/site-packages/scripts/start_parallel_jobs.py]"/>
  <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling"
   help="suppress polling of jobs and merging of results upon completion [default: False]"/>
  <param name="job_prefix" type="text"  label="job_prefix"
   help="job prefix [default: descriptive prefix + random chars]"/>
  <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp"
   help="full path to python executable [default: python]"/>
  <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep"
   help="Number of seconds to sleep between checks for run  completion when polling runs [default: 60]"/>
 </inputs>
 <outputs>
  
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>