Mercurial > repos > jjohnson > qiime
comparison supervised_learning.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
| author | Jim Johnson <jj@umn.edu> |
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| date | Sun, 17 Jul 2011 10:30:11 -0500 |
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| -1:000000000000 | 0:e5c3175506b7 |
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| 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="text" 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 |