<tool id="split_libraries_illumina" name="split_libraries_illumina" version="1.2.0">
 <description>Script for processing raw Illumina Genome Analyzer II data.</description>
 <requirements>
  <requirement type="binary">split_libraries_illumina.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  split_libraries_illumina.py
  --mapping_fp=$mapping_fp
  --five_prime_read_fp=$five_prime_read_fp
  --three_prime_read_fp=$three_prime_read_fp
  --output_dir=$__new_file_path__
  $store_unassigned
  --quality_threshold=$quality_threshold
  --max_bad_run_length=$max_bad_run_length
  --min_per_read_length=$min_per_read_length
  --sequence_max_n=$sequence_max_n
  --start_seq_id=$start_seq_id
  $rev_comp_barcode
  $barcode_in_header
 </command>
 <inputs>
  <param name="mapping_fp" type="data" format="tabular" label="mapping_fp"
   help="the mapping filepath [REQUIRED]"/>
  <param name="five_prime_read_fp" type="data" format="txt" label="five_prime_read_fp"
   help="the 5' read filepath [default: ('NO', 'DEFAULT')]"/>
  <param name="three_prime_read_fp" type="data" format="txt" label="three_prime_read_fp"
   help="the 3' read filepath [default: ('NO', 'DEFAULT')]"/>
  <param name="store_unassigned" type="boolean" truevalue="--store_unassigned" falsevalue="" checked="false" label="store_unassigned"
   help="store seqs which can't be assigned to samples because of unknown barcodes [default: False]"/>
  <param name="quality_threshold" type="float" value="1e-05" label="quality_threshold"
   help="max base call error probability to consider high-quality (probability of base call being error, so values closer to 1 mean that the base call is more likely to be erroneous) [default: 1e-05]"/>
  <param name="max_bad_run_length" type="integer" value="1" label="max_bad_run_length"
   help="max number of consecutive low quality base calls allowed before truncating a read [default: 1; the read is trucated at thesecond low quality call]"/>
  <param name="min_per_read_length" type="integer" value="75" label="min_per_read_length"
   help="min number of consecutive high quality base calls to includea read (per single end read) [default: 75]"/>
  <param name="sequence_max_n" type="integer" value="0" label="sequence_max_n"
   help="maximum number of N characters allowed in a sequence to retain it -- this is applied after quality trimming, and is total over combined paired end reads if applicable [default: 0]"/>
  <param name="start_seq_id" type="integer" value="0" label="start_seq_id"
   help="start seq_ids as ascending integers beginning with start_seq_id[default: 0]"/>
  <param name="rev_comp_barcode" type="boolean" truevalue="--rev_comp_barcode" falsevalue="" checked="false" label="rev_comp_barcode"
   help="reverse compliment barcodes before lookup[default: False]"/>
  <param name="barcode_in_header" type="boolean" truevalue="--barcode_in_header" falsevalue="" checked="false" label="barcode_in_header"
   help="barcode is in header line (rather than beginning of sequence)[default: False]"/>
 </inputs>
 <outputs>
  
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>