<tool id="check_id_map" name="check_id_map" version="2.0.0">
 <description>Checks user's metadata mapping file for required data, valid format</description>
 <requirements>
  <requirement type="binary">check_id_map.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_outputdir='$log.extra_files_path'
  --galaxy_datasets='^\S+_corrected\.txt$:'$corrected_mapping,'^\S+\.log:'$log
  check_id_map.py
  --map=$map
  --output_dir='$log.extra_files_path'
  --char_replace=$char_replace
  $not_barcoded
  $variable_len_barcodes
  $disable_primer_check
  $verbose
  #if $added_demultiplex_field != None and $added_demultiplex_field.__str__ != "":
  --added_demultiplex_field=$added_demultiplex_field
  #end if
 </command>
 <inputs>
  <param name="map" type="data" format="tabular" label="map"
   help="Metadata mapping file filepath [REQUIRED]"/>
  <param name="char_replace" type="text" value="_" label="char_replace"
   help="Changes the default character used to replace invalid characters found in the mapping file.  Must be a valid character (alphanumeric or underscore).  NOT IMPLEMENTED CURRENTLY [default: _]"/>
  <param name="not_barcoded" type="boolean" truevalue="--not_barcoded" falsevalue="" checked="false" label="not_barcoded"
   help="Use this option if barcodes are not present. [default: False]"/>
  <param name="variable_len_barcodes" type="boolean" truevalue="--variable_len_barcodes" falsevalue="" checked="false" label="variable_len_barcodes"
   help="Use this option if variable length barcodes are present to suppress warnings about barcodes of unequal length. [default: False]"/>
  <param name="disable_primer_check" type="boolean" truevalue="--disable_primer_check" falsevalue="" checked="false" label="disable_primer_check"
   help="Use this option to disable checks for primers. [default: False]"/>
  <param name="verbose" type="boolean" truevalue="" falsevalue="--verbose" checked="false" label="verbose"
   help="Turn on this flag to disable verbose output.  [default: True]"/>
  <param name="added_demultiplex_field" type="text" value="" label="added_demultiplex_field"
   help="Use this option to add a field to use in the mapping file as an additional demultiplexing option to the barcode. All combinations of barcodes and the values in these fields must be unique. The fields must contain values that can be parsed from the fasta labels such as 'plate==R_2008_12_09'. In this case, 'plate' would be the column header and 'R_2008_12_09' would be the field data (minus quotes) in the mapping file. To use the run prefix from the fasta label, such as '>FLP3FBN01ELBSX', where 'FLP3FBN01' is generated from the run ID, enter 'run_prefix' in the field and set the run prefix to be used as the data under the column header 'run_prefix'. [default: None]"/>
 </inputs>
 <outputs>
   <data format="txt" name="log"/>
   <data format="tabular" name="corrected_mapping" label="${tool.name} on ${on_string}: corrected_mapping"/>
 </outputs>
 <tests>
 </tests>
 <help>For more information, see check_id_map_ in the Qiime documentation.
 
Updated and validated 01/19/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA

Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
 
 .. _check_id_map: http://qiime.org/scripts/check_id_map.html</help>
</tool>