<tool id="filter_alignment" name="filter_alignment" version="2.0.0">
 <description>Filter sequence alignment by removing highly variable regions</description>
 <requirements>
  <requirement type="binary">filter_alignment.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  ## --galaxy_tmpdir='$__new_file_path__'
  --galaxy_outputdir='$pfiltered_fasta.extra_files_path'
  --galaxy_datasets='^\S+_pfiltered\.\S+$:'$pfiltered_fasta
  filter_alignment.py
  --input_fasta_file=$input_fasta_file
  --output_dir='$pfiltered_fasta.extra_files_path'
  --lane_mask_fp=$lane_mask_fp
  $suppress_lane_mask_filter
  --allowed_gap_frac=$allowed_gap_frac
  $remove_outliers
  --threshold=$threshold
  #if $entropy_threshold != 0.0:
  --entropy_threshold=$entropy_threshold
  #end if
 </command>
 <inputs>
  <param name="input_fasta_file" type="data" format="align" label="input_fasta_file"
   help="input FASTA file (usually output from align_seqs)  [REQUIRED]"/>
  <param name="lane_mask_fp" type="data" format="filter" label="lane_mask_fp"
   help="path to lanemask file (usually lanemask_in_1s_and_0s.txt)"/>
  <param name="suppress_lane_mask_filter" type="boolean" truevalue="--suppress_lane_mask_filter" falsevalue="" checked="false" label="suppress_lane_mask_filter"
   help="suppress lane mask filtering (necessary to turn off lane-mask-based filtering when a qiime_config default is  provided for --lane_mask_fp) [default: False]"/>
  <param name="allowed_gap_frac" type="float" value="0.999999" label="allowed_gap_frac"
   help="gap filter threshold, filters positions which are gaps in } allowed_gap_frac of the sequences [default: 0.999999]"/>
  <param name="remove_outliers" type="boolean" truevalue="--remove_outliers" falsevalue="" checked="false" label="remove_outliers"
   help="remove seqs very dissimilar to the alignment consensus (see --threshold).  [default: False]"/>
  <param name="threshold" type="float" value="3.0" label="threshold"
   help="with -r, remove seqs whose dissimilarity to the consensus sequence is approximately } x standard devaitions above the mean of the sequences [default: 3.0]"/>
  <param name="entropy_threshold" type="float" value="0" label="entropy_threshold" help="Sets percent threshold for removing base positions with the highest entropy. For example, if 0.10 were specified, the top 10% most entropic base positions would be filtered. If this value is used, any lane mask supplied will be ignored. Entropy filtered occurs after gap filtering. [default: None]"/>
 </inputs>
 <outputs>
  <data format="align" name="pfiltered_fasta" label="${tool.name} on ${on_string}: pfiltered.fasta"/>
 </outputs>
 <tests>
 </tests>
 <help>For more information, see filter_alignment_ 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

.. _filter_alignment: http://qiime.org/scripts/filter_alignment.html</help>
</tool>