diff supervised_learning.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/supervised_learning.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,62 @@
+<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>
+