Mercurial > repos > bgruening > eden_vectorizer

comparison main_macros.xml @ 5:4338e8aac25b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
author bgruening
date Thu, 23 Jun 2016 15:27:02 -0400
parents 49857bc1b594
children
comparison
equal deleted inserted replaced
4:3df106e75b33 5:4338e8aac25b
1 <macros> 1 <macros>
2 <token name="@VERSION@">0.9</token> 2 <token name="@VERSION@">0.9</token>
3
4 <token name="@COLUMNS_FUNCTION@">
5 def columns(f,c):
6 data = pandas.read_csv(f, sep='\t', header=None, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False)
7 cols = c.split (',')
8 cols = map(int, cols)
9 cols = list(map(lambda x: x - 1, cols))
10 y = data.iloc[:,cols].values
11 return y
12 </token>
3 13
4 <xml name="python_requirements"> 14 <xml name="python_requirements">
5 <requirements> 15 <requirements>
6 <requirement type="package" version="0.2.1b">eden</requirement> 16 <requirement type="package" version="0.2.1b">eden</requirement>
7 <yield /> 17 <yield />
217 <xml name="pos_label" token_default_value=""> 227 <xml name="pos_label" token_default_value="">
218 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/> 228 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
219 </xml> 229 </xml>
220 230
221 <xml name="average"> 231 <xml name="average">
222 <param argument="average" type="select" optional="True" label="Averaging type" help=" "> 232 <param argument="average" type="select" optional="true" label="Averaging type" help=" ">
223 <option value="binary" selected="true" help="Only report results for the class specified by pos_label. Applicable only on binary classification.">binary</option>
224 <option value="micro" help="Calculate metrics globally by counting the total true positives, false negatives and false positives.">micro</option> 233 <option value="micro" help="Calculate metrics globally by counting the total true positives, false negatives and false positives.">micro</option>
225 <option value="samples" help="Calculate metrics for each instance, and find their average (only meaningful for multilabel).">samples</option> 234 <option value="samples" help="Calculate metrics for each instance, and find their average (only meaningful for multilabel).">samples</option>
226 <!--option value="macro" help=""></option--> 235 <!--option value="macro" help=""></option-->
227 <!--option value="weighted" help=""></option--> 236 <!--option value="weighted" help=""></option-->
237 <yield/>
228 </param> 238 </param>
229 </xml> 239 </xml>
230 240
231 <xml name="beta"> 241 <xml name="beta">
232 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/> 242 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>
244 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/> 254 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
245 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/> 255 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
246 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/> 256 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
247 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/> 257 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
248 <yield/> 258 <yield/>
259 </xml>
260
261
262 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False">
263 <conditional name="true_columns">
264 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:">
265 <option value="tabular" selected="true">Tabular</option>
266 <option value="sparse">Sparse</option>
267 </param>
268 <when value="tabular">
269 <param name="infile1" type="data" label="@LABEL1@"/>
270 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:"/>
271 </when>
272 <when value="sparse">
273 <param name="infile1" type="data" format="txt" label="@LABEL1@"/>
274 </when>
275 </conditional>
276 <conditional name="predicted_columns">
277 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:">
278 <option value="tabular" selected="true">Tabular</option>
279 <option value="sparse">Sparse</option>
280 </param>
281 <when value="tabular">
282 <param name="infile2" type="data" label="@LABEL2@"/>
283 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
284 </when>
285 <when value="sparse">
286 <param name="infile2" type="data" format="txt" label="@LABEL1@"/>
287 </when>
288 </conditional>
289 </xml>
290
291 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False">
292 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/>
293 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select the target column:"/>
294 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/>
295 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
249 </xml> 296 </xml>
250 297
251 <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format."> 298 <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format.">
252 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):"> 299 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
253 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/> 300 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>