|
2
|
1 <tool id="supervised_learning" name="supervised_learning" version="1.2.1">
|
|
|
2 <description>Run supervised classification using OTUs as predictors and a mapping file category as class labels.</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="binary">supervised_learning.py</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command interpreter="python">
|
|
|
7 qiime_wrapper.py
|
|
|
8 --galaxy_tmpdir='$__new_file_path__'
|
|
|
9 supervised_learning.py
|
|
|
10 --input_data=$input_data
|
|
|
11 --mapping_file=$mapping_file
|
|
|
12 --category=$category
|
|
|
13 --output_dir=$__new_file_path__
|
|
|
14 --method=$method
|
|
|
15 $force
|
|
|
16 --param_file=$param_file
|
|
|
17 $show_params
|
|
|
18 --filter_type=$filter_type
|
|
|
19 --filter_min=$filter_min
|
|
|
20 --filter_max=$filter_max
|
|
|
21 --filter_step=$filter_step
|
|
|
22 --filter_reps=$filter_reps
|
|
|
23 $keepfiles
|
|
|
24 </command>
|
|
|
25 <inputs>
|
|
|
26 <param name="input_data" type="data" label="input_data"
|
|
|
27 help="Input data file containing predictors (e.g. otu table) [REQUIRED]"/>
|
|
|
28 <param name="mapping_file" type="data" format="tabular" label="mapping_file"
|
|
|
29 help="File containing meta data (response variables) [REQUIRED]"/>
|
|
|
30 <param name="category" type="text" label="category"
|
|
|
31 help="Name of meta data category to predict [REQUIRED]"/>
|
|
|
32 <param name="method" type="text" value="random_forest" label="method"
|
|
|
33 help="Comma-separated list of supervised learning methods to apply. Currently one option is available: 'random_forest' [default: random_forest]."/>
|
|
|
34 <param name="force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="force"
|
|
|
35 help="Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: ('NO', 'DEFAULT')]"/>
|
|
|
36 <param name="param_file" type="data" format="txt" label="param_file"
|
|
|
37 help="file containing parameters for the supervised learning model inference [default: %default]"/>
|
|
|
38 <param name="show_params" type="boolean" truevalue="--show_params" falsevalue="" checked="false" label="show_params"
|
|
|
39 help="show sample parameters file for a given method [default: False]"/>
|
|
|
40 <param name="filter_type" type="text" label="filter_type"
|
|
|
41 help="type of filter to use. Currently one is available: BSSWSS. [default: %default]"/>
|
|
|
42 <param name="filter_min" type="integer" value="2" label="filter_min"
|
|
|
43 help="minimum number of features to try with filter [default: 2]"/>
|
|
|
44 <param name="filter_max" type="integer" value="20" label="filter_max"
|
|
|
45 help="maximum number of features to try with filter [default: 20]"/>
|
|
|
46 <param name="filter_step" type="integer" value="1" label="filter_step"
|
|
|
47 help="step increment for number of features to try with filter [default: 1]"/>
|
|
|
48 <param name="filter_reps" type="integer" value="10" label="filter_reps"
|
|
|
49 help="Number of models to train for estimating filter error [default: 10]"/>
|
|
|
50 <param name="keepfiles" type="boolean" truevalue="--keepfiles" falsevalue="" checked="false" label="keepfiles"
|
|
|
51 help="Keep R-formatted input files [default: ('NO', 'DEFAULT')]"/>
|
|
|
52 </inputs>
|
|
|
53 <outputs>
|
|
|
54
|
|
|
55 </outputs>
|
|
|
56 <tests>
|
|
|
57 </tests>
|
|
|
58 <help>
|
|
|
59
|
|
|
60 </help>
|
|
|
61 </tool>
|
|
|
62
|
