Mercurial > repos > bgruening > sklearn_numeric_clustering

comparison main_macros.xml @ 3:a8951d76b7d2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
author bgruening
date Fri, 03 Jun 2016 13:57:01 -0400
parents fe2d62fbf47b
children 7dc70333811d
comparison
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2:fe2d62fbf47b 3:a8951d76b7d2
8 </requirements> 8 </requirements>
9 </xml> 9 </xml>
10 10
11 <xml name="macro_stdio"> 11 <xml name="macro_stdio">
12 <stdio> 12 <stdio>
13 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 13 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
14 </stdio> 14 </stdio>
15 </xml> 15 </xml>
16 16
17 17
18 <!--Generic interface--> 18 <!--Generic interface-->
21 <param name="selected_task" type="select" label="Select a Classification Task"> 21 <param name="selected_task" type="select" label="Select a Classification Task">
22 <option value="train" selected="true">Train a model</option> 22 <option value="train" selected="true">Train a model</option>
23 <option value="load">Load a model and predict</option> 23 <option value="load">Load a model and predict</option>
24 </param> 24 </param>
25 <when value="load"> 25 <when value="load">
26 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file." /> 26 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
27 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/> 27 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
28 <conditional name="prediction_options"> 28 <conditional name="prediction_options">
29 <param name="prediction_option" type="select" label="Select the type of prediction"> 29 <param name="prediction_option" type="select" label="Select the type of prediction">
30 <option value="predict">Predict class labels</option> 30 <option value="predict">Predict class labels</option>
31 <option value="advanced">Include advanced options</option> 31 <option value="advanced">Include advanced options</option>
35 <when value="advanced"> 35 <when value="advanced">
36 </when> 36 </when>
37 </conditional> 37 </conditional>
38 </when> 38 </when>
39 <when value="train"> 39 <when value="train">
40 <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)" /> 40 <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)"/>
41 <conditional name="selected_algorithms"> 41 <conditional name="selected_algorithms">
42 <yield /> 42 <yield />
43 </conditional> 43 </conditional>
44 </when> 44 </when>
45 </conditional> 45 </conditional>
50 <param name="selected_task" type="select" label="Select a Classification Task"> 50 <param name="selected_task" type="select" label="Select a Classification Task">
51 <option value="train" selected="true">Train a model</option> 51 <option value="train" selected="true">Train a model</option>
52 <option value="load">Load a model and predict</option> 52 <option value="load">Load a model and predict</option>
53 </param> 53 </param>
54 <when value="load"> 54 <when value="load">
55 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file." /> 55 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
56 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/> 56 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
57 <conditional name="prediction_options"> 57 <conditional name="prediction_options">
58 <param name="prediction_option" type="select" label="Select the type of prediction"> 58 <param name="prediction_option" type="select" label="Select the type of prediction">
59 <option value="predict">Predict class labels</option> 59 <option value="predict">Predict class labels</option>
60 <option value="advanced">Include advanced options</option> 60 <option value="advanced">Include advanced options</option>
271 </when> 271 </when>
272 <when value="sparse"> 272 <when value="sparse">
273 <expand macro="sparse_target"/> 273 <expand macro="sparse_target"/>
274 </when> 274 </when>
275 </conditional> 275 </conditional>
276 </xml>
277
278 <xml name="multitype_input" token_format="tabular" token_help="All datasets with tabular format are supporetd.">
279 <param name="infile_transform" type="data" format="@FORMAT@" label="Select a dataset to transform:" help="@HELP@"/>
276 </xml> 280 </xml>
277 281
278 282
279 <!--Advanced options--> 283 <!--Advanced options-->
280 <xml name="nn_advanced_options"> 284 <xml name="nn_advanced_options">
523 </when> 527 </when>
524 </xml> 528 </xml>
525 529
526 <xml name="sparse_preprocessors"> 530 <xml name="sparse_preprocessors">
527 <param name="selected_pre_processor" type="select" label="Select a preprocessor:"> 531 <param name="selected_pre_processor" type="select" label="Select a preprocessor:">
528 <option value="StandardScaler" selected="true">Standardize features by removing the mean and scaling to unit variance</option> 532 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option>
529 <option value="Binarizer">Binarize data</option> 533 <option value="Binarizer">Binarizer (Binarizes data)</option>
530 <option value="Imputer">Complete missing values</option> 534 <option value="Imputer">Imputer (Completes missing values)</option>
531 <option value="MaxAbsScaler">Scale features by their maximum absolute value</option> 535 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option>
532 <option value="Normalizer">Normalize samples individually to unit norm</option> 536 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option>
533 <yield/> 537 <yield/>
534 </param> 538 </param>
535 </xml> 539 </xml>
536 540
537 <xml name="sparse_preprocessor_options"> 541 <xml name="sparse_preprocessor_options">
538 <when value="Binarizer"> 542 <when value="Binarizer">
543 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
539 <section name="options" title="Advanced Options" expanded="False"> 544 <section name="options" title="Advanced Options" expanded="False">
540 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing binarization" help=" "/> 545 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing binarization" help=" "/>
541 <param argument="threshold" type="float" optional="true" value="0.0" label="Threshold" help="Feature values below or equal to this are replaced by 0, above it by 1. Threshold may not be less than 0 for operations on sparse matrices. "/> 546 <param argument="threshold" type="float" optional="true" value="0.0" label="Threshold" help="Feature values below or equal to this are replaced by 0, above it by 1. Threshold may not be less than 0 for operations on sparse matrices. "/>
542 </section> 547 </section>
543 </when> 548 </when>
544 <when value="Imputer"> 549 <when value="Imputer">
545 <section name="options" title="Advanced Options" expanded="False"> 550 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
546 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing imputation" help=" "/> 551 <section name="options" title="Advanced Options" expanded="False">
547 <param argument="strategy" type="select" optional="true" label="Imputation strategy" help=" "> 552 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing imputation" help=" "/>
548 <option value="mean" selected="true">Replace missing values using the mean along the axis</option> 553 <param argument="strategy" type="select" optional="true" label="Imputation strategy" help=" ">
549 <option value="median">Replace missing values using the median along the axis</option> 554 <option value="mean" selected="true">Replace missing values using the mean along the axis</option>
550 <option value="most_frequent">Replace missing using the most frequent value along the axis</option> 555 <option value="median">Replace missing values using the median along the axis</option>
551 </param> 556 <option value="most_frequent">Replace missing using the most frequent value along the axis</option>
552 <param argument="missing_values" type="text" optional="true" value="NaN" label="Placeholder for missing values" help="For missing values encoded as numpy.nan, use the string value “NaN”"/> 557 </param>
553 <param argument="axis" type="select" optional="true" label="The axis along which to impute" help=" "> 558 <param argument="missing_values" type="text" optional="true" value="NaN" label="Placeholder for missing values" help="For missing values encoded as numpy.nan, use the string value “NaN”"/>
554 <option value="0" selected="true">Impute along columns</option> 559 <param argument="axis" type="boolean" optional="true" truevalue="1" falsevalue="0" label="Impute along axis = 1" help="If fasle, axis = 0 is selected for imputation. "/>
555 <option value="1">Impute along rows</option> 560 <!--param argument="axis" type="select" optional="true" label="The axis along which to impute" help=" ">
556 </param> 561 <option value="0" selected="true">Impute along columns</option>
557 </section> 562 <option value="1">Impute along rows</option>
563 </param-->
564 </section>
558 </when> 565 </when>
559 <when value="StandardScaler"> 566 <when value="StandardScaler">
560 <section name="options" title="Advanced Options" expanded="False"> 567 <expand macro="multitype_input"/>
561 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for performing inplace scaling" help=" "/> 568 <section name="options" title="Advanced Options" expanded="False">
562 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Center the data before scaling" help=" "/> 569 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for performing inplace scaling" help=" "/>
563 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Scale the data to unit variance (or unit standard deviation)" help=" "/> 570 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Center the data before scaling" help=" "/>
564 </section> 571 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Scale the data to unit variance (or unit standard deviation)" help=" "/>
572 </section>
565 </when> 573 </when>
566 <when value="MaxAbsScaler"> 574 <when value="MaxAbsScaler">
567 <section name="options" title="Advanced Options" expanded="False"> 575 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
568 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing scaling" help=" "/> 576 <section name="options" title="Advanced Options" expanded="False">
569 </section> 577 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing scaling" help=" "/>
578 </section>
570 </when> 579 </when>
571 <when value="Normalizer"> 580 <when value="Normalizer">
572 <section name="options" title="Advanced Options" expanded="False"> 581 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
573 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" "> 582 <section name="options" title="Advanced Options" expanded="False">
574 <option value="l1" selected="true">l1</option> 583 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" ">
575 <option value="l2">l2</option> 584 <option value="l1" selected="true">l1</option>
576 <option value="max">max</option> 585 <option value="l2">l2</option>
577 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing row normalization" help=" "/> 586 <option value="max">max</option>
578 </param> 587 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing row normalization" help=" "/>
579 </section> 588 </param>
589 </section>
580 </when> 590 </when>
581 <yield/> 591 <yield/>
582 </xml> 592 </xml>
583 593
584 594