view supervised_learning.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="supervised_learning" name="supervised_learning" version="1.2.1">
 <description>Run supervised classification using OTUs as predictors and a mapping file category as class labels.</description>
 <requirements>
  <requirement type="binary">supervised_learning.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  supervised_learning.py
  --input_data=$input_data
  --mapping_file=$mapping_file
  --category=$category
  --output_dir=$__new_file_path__
  --method=$method
  $force
  --param_file=$param_file
  $show_params
  --filter_type=$filter_type
  --filter_min=$filter_min
  --filter_max=$filter_max
  --filter_step=$filter_step
  --filter_reps=$filter_reps
  $keepfiles
 </command>
 <inputs>
  <param name="input_data" type="text"  label="input_data"
   help="Input data file containing predictors (e.g. otu table) [REQUIRED]"/>
  <param name="mapping_file" type="data" format="tabular" label="mapping_file"
   help="File containing meta data (response variables) [REQUIRED]"/>
  <param name="category" type="text"  label="category"
   help="Name of meta data category to predict [REQUIRED]"/>
  <param name="method" type="text" value="random_forest" label="method"
   help="Comma-separated list of supervised learning methods to apply. Currently one option is available: 'random_forest' [default: random_forest]."/>
  <param name="force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="force"
   help="Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: ('NO', 'DEFAULT')]"/>
  <param name="param_file" type="data" format="txt" label="param_file"
   help="file containing parameters for the supervised learning model inference [default: %default]"/>
  <param name="show_params" type="boolean" truevalue="--show_params" falsevalue="" checked="false" label="show_params"
   help="show sample parameters file for a given method [default: False]"/>
  <param name="filter_type" type="text"  label="filter_type"
   help="type of filter to use. Currently one is available: BSSWSS. [default: %default]"/>
  <param name="filter_min" type="integer" value="2" label="filter_min"
   help="minimum number of features to try with filter [default: 2]"/>
  <param name="filter_max" type="integer" value="20" label="filter_max"
   help="maximum number of features to try with filter [default: 20]"/>
  <param name="filter_step" type="integer" value="1" label="filter_step"
   help="step increment for number of features to try with filter [default: 1]"/>
  <param name="filter_reps" type="integer" value="10" label="filter_reps"
   help="Number of models to train for estimating filter error [default: 10]"/>
  <param name="keepfiles" type="boolean" truevalue="--keepfiles" falsevalue="" checked="false" label="keepfiles"
   help="Keep R-formatted input files [default: ('NO', 'DEFAULT')]"/>
 </inputs>
 <outputs>
  
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>