<tool id="parallel_identify_chimeric_seqs" name="parallel_identify_chimeric_seqs" version="1.2.0">
 <description>Parallel chimera detection</description>
 <requirements>
  <requirement type="binary">parallel_identify_chimeric_seqs.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  parallel_identify_chimeric_seqs.py
  --input_fasta_fp=$input_fasta_fp
  --aligned_reference_seqs_fp=$aligned_reference_seqs_fp
  --id_to_taxonomy_fp=$id_to_taxonomy_fp
  --reference_seqs_fp=$reference_seqs_fp
  --blast_db=$blast_db
  --chimera_detection_method=$chimera_detection_method
  --num_fragments=$num_fragments
  --taxonomy_depth=$taxonomy_depth
  --max_e_value=$max_e_value
  --min_div_ratio=$min_div_ratio
  --output_fp=$output_fp
  --identify_chimeric_seqs_fp=$identify_chimeric_seqs_fp
  --jobs_to_start=$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="aligned_reference_seqs_fp" type="data" format="txt" label="aligned_reference_seqs_fp"
   help="Path to (Py)Nast aligned reference sequences. REQUIRED when method ChimeraSlayer [default: ('NO', 'DEFAULT')]"/>
  <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. [default: ('NO', 'DEFAULT'); REQUIRED when method is blast_fragments]"/>
  <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: ('NO', 'DEFAULT'); REQUIRED when method blast_fragments if no blast_db is provided;]"/>
  <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: ('NO', 'DEFAULT')]"/>
  <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>
  <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="taxonomy_depth" type="integer" value="4" label="taxonomy_depth"
   help="Number of taxonomic divisions to consider when comparing taxonomy assignments [default: 4]"/>
  <param name="max_e_value" type="float" value="1e-30" label="max_e_value"
   help="Max e-value to assign taxonomy [default: 1e-30]"/>
  <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: %default]"/>
  <param name="identify_chimeric_seqs_fp" type="data" format="txt" label="identify_chimeric_seqs_fp"
   help="full path to scripts/identify_chimeric_seqs.py [default: /usr/local/lib/python2.6/site-packages/scripts/identify_chimeric_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>
  <data format="txt" name="output_fp"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>