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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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1 <tool id="supervised_learning" name="supervised_learning" version="1.2.1">
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2 <description>Run supervised classification using OTUs as predictors and a mapping file category as class labels.</description>
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3 <requirements>
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4 <requirement type="binary">supervised_learning.py</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 qiime_wrapper.py
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8 --galaxy_tmpdir='$__new_file_path__'
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9 supervised_learning.py
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10 --input_data=$input_data
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11 --mapping_file=$mapping_file
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12 --category=$category
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13 --output_dir=$__new_file_path__
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14 --method=$method
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15 $force
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16 --param_file=$param_file
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17 $show_params
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18 --filter_type=$filter_type
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19 --filter_min=$filter_min
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20 --filter_max=$filter_max
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21 --filter_step=$filter_step
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22 --filter_reps=$filter_reps
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23 $keepfiles
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24 </command>
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25 <inputs>
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26 <param name="input_data" type="text" label="input_data"
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27 help="Input data file containing predictors (e.g. otu table) [REQUIRED]"/>
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28 <param name="mapping_file" type="data" format="tabular" label="mapping_file"
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29 help="File containing meta data (response variables) [REQUIRED]"/>
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30 <param name="category" type="text" label="category"
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31 help="Name of meta data category to predict [REQUIRED]"/>
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32 <param name="method" type="text" value="random_forest" label="method"
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33 help="Comma-separated list of supervised learning methods to apply. Currently one option is available: 'random_forest' [default: random_forest]."/>
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34 <param name="force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="force"
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35 help="Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: ('NO', 'DEFAULT')]"/>
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36 <param name="param_file" type="data" format="txt" label="param_file"
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37 help="file containing parameters for the supervised learning model inference [default: %default]"/>
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38 <param name="show_params" type="boolean" truevalue="--show_params" falsevalue="" checked="false" label="show_params"
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39 help="show sample parameters file for a given method [default: False]"/>
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40 <param name="filter_type" type="text" label="filter_type"
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41 help="type of filter to use. Currently one is available: BSSWSS. [default: %default]"/>
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42 <param name="filter_min" type="integer" value="2" label="filter_min"
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43 help="minimum number of features to try with filter [default: 2]"/>
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44 <param name="filter_max" type="integer" value="20" label="filter_max"
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45 help="maximum number of features to try with filter [default: 20]"/>
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46 <param name="filter_step" type="integer" value="1" label="filter_step"
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47 help="step increment for number of features to try with filter [default: 1]"/>
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48 <param name="filter_reps" type="integer" value="10" label="filter_reps"
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49 help="Number of models to train for estimating filter error [default: 10]"/>
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50 <param name="keepfiles" type="boolean" truevalue="--keepfiles" falsevalue="" checked="false" label="keepfiles"
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51 help="Keep R-formatted input files [default: ('NO', 'DEFAULT')]"/>
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52 </inputs>
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53 <outputs>
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54
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55 </outputs>
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56 <tests>
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57 </tests>
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58 <help>
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59
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60 </help>
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61 </tool>
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