view check_id_map.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="check_id_map" name="check_id_map" version="1.2.0">
 <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
  $verbose
 </command>
 <inputs>
  <param name="map" type="data" format="tabular" label="map"
   help="Metadata mapping file filepath [REQUIRED]"/>
  <param name="char_replace" type="text" value="_" label="char_replace"
   help="Changes the default character used to replace invalid characters found in the mapping file.  Must be a valid character (alphanumeric or underscore).  NOT IMPLEMENTED CURRENTLY [default: _]"/>
  <param name="not_barcoded" type="boolean" truevalue="--not_barcoded" falsevalue="" checked="false" label="not_barcoded"
   help="Use -b if barcodes are not present. [default: False]"/>
  <param name="variable_len_barcodes" type="boolean" truevalue="--variable_len_barcodes" falsevalue="" checked="false" label="variable_len_barcodes"
   help="Use -B if variable length barcodes are present to suppress warnings about barcodes of unequal length. [default: False]"/>
  <param name="disable_primer_check" type="boolean" truevalue="--disable_primer_check" falsevalue="" checked="false" label="disable_primer_check"
   help="Use -p to disable checks for primers. [default: False]"/>
  <param name="verbose" type="boolean" truevalue="" falsevalue="--verbose" checked="false" label="verbose"
   help="Turn on this flag to disable verbose output.  [default: True]"/>
 </inputs>
 <outputs>
   <data format="txt" name="log"/>
   <data format="tabular" name="corrected_mapping" label="${tool.name} on ${on_string}: corrected_mapping"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>