Mercurial > repos > bgruening > sklearn_discriminant_classifier
diff discriminant.xml @ 35:eeaf989f1024 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
| author | bgruening |
|---|---|
| date | Tue, 13 Apr 2021 18:09:01 +0000 |
| parents | 64b771b1471a |
| children | d769d83ec796 |
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--- a/discriminant.xml Thu Oct 01 20:44:13 2020 +0000 +++ b/discriminant.xml Tue Apr 13 18:09:01 2021 +0000 @@ -1,20 +1,20 @@ -<tool id="sklearn_discriminant_classifier" name="Discriminant Analysis" version="@VERSION@"> +<tool id="sklearn_discriminant_classifier" name="Discriminant Analysis" version="@VERSION@" profile="20.05"> <description></description> <macros> <import>main_macros.xml</import> <!--macro name="priors"--> </macros> - <expand macro="python_requirements"/> - <expand macro="macro_stdio"/> + <expand macro="python_requirements" /> + <expand macro="macro_stdio" /> <version_command>echo "@VERSION@"</version_command> <command><![CDATA[ python "$discriminant_script" '$inputs' ]]> </command> <configfiles> - <inputs name="inputs"/> + <inputs name="inputs" /> <configfile name="discriminant_script"> -<![CDATA[ + <![CDATA[ import json import numpy as np import pandas @@ -65,7 +65,7 @@ <option value="QuadraticDiscriminantAnalysis">Quadratic Discriminant Classifier</option> </param> <when value="LinearDiscriminantAnalysis"> - <expand macro="sl_mixed_input"/> + <expand macro="sl_mixed_input" /> <section name="options" title="Advanced Options" expanded="False"> <param argument="solver" type="select" optional="true" label="Solver" help=""> <option value="svd" selected="true">Singular Value Decomposition</option> @@ -74,83 +74,80 @@ </param> <!--param name="shrinkage"--> <!--expand macro="priors"/--> - <param argument="n_components" type="integer" optional="true" value="" label="Number of components" - help="Number of components for dimensionality reduction. ( always less than n_classes - 1 )"/> - <expand macro="tol" default_value="0.0001" help_text="Rank estimation threshold used in SVD solver."/> - <param argument="store_covariance" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" - label="Store covariance" help="Compute class covariance matrix."/> + <param argument="n_components" type="integer" optional="true" value="" label="Number of components" help="Number of components for dimensionality reduction. ( always less than n_classes - 1 )" /> + <expand macro="tol" default_value="0.0001" help_text="Rank estimation threshold used in SVD solver." /> + <param argument="store_covariance" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Store covariance" help="Compute class covariance matrix." /> </section> </when> <when value="QuadraticDiscriminantAnalysis"> - <expand macro="sl_mixed_input"/> + <expand macro="sl_mixed_input" /> <section name="options" title="Advanced Options" expanded="False"> <!--expand macro="priors"/--> - <param argument="reg_param" type="float" optional="true" value="0.0" label="Regularization coefficient" help="Covariance estimate regularizer."/> - <expand macro="tol" default_value="0.00001" help_text="Rank estimation threshold used in SVD solver."/> - <param argument="store_covariance" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" - label="Store covariances" help="Compute class covariance matrixes."/> + <param argument="reg_param" type="float" optional="true" value="0.0" label="Regularization coefficient" help="Covariance estimate regularizer." /> + <expand macro="tol" default_value="0.00001" help_text="Rank estimation threshold used in SVD solver." /> + <param argument="store_covariance" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Store covariances" help="Compute class covariance matrixes." /> </section> </when> </expand> </inputs> - <expand macro="output"/> + <expand macro="output" /> <tests> <test> - <param name="infile1" value="train.tabular" ftype="tabular"/> - <param name="infile2" value="train.tabular" ftype="tabular"/> - <param name="header1" value="True"/> - <param name="header2" value="True"/> - <param name="col1" value="1,2,3,4"/> - <param name="col2" value="5"/> - <param name="selected_task" value="train"/> - <param name="selected_algorithm" value="LinearDiscriminantAnalysis"/> + <param name="infile1" value="train.tabular" ftype="tabular" /> + <param name="infile2" value="train.tabular" ftype="tabular" /> + <param name="header1" value="True" /> + <param name="header2" value="True" /> + <param name="col1" value="1,2,3,4" /> + <param name="col2" value="5" /> + <param name="selected_task" value="train" /> + <param name="selected_algorithm" value="LinearDiscriminantAnalysis" /> <param name="solver" value="svd" /> - <param name="store_covariance" value="True"/> - <output name="outfile_fit" file="lda_model01" compare="sim_size" delta="1"/> + <param name="store_covariance" value="True" /> + <output name="outfile_fit" file="lda_model01" compare="sim_size" delta="1" /> </test> <test> - <param name="infile1" value="train.tabular" ftype="tabular"/> - <param name="infile2" value="train.tabular" ftype="tabular"/> - <param name="header1" value="True"/> - <param name="header2" value="True"/> - <param name="col1" value="1,2,3,4"/> - <param name="col2" value="5"/> - <param name="selected_task" value="train"/> - <param name="selected_algorithm" value="LinearDiscriminantAnalysis"/> - <param name="solver" value="lsqr"/> - <output name="outfile_fit" file="lda_model02" compare="sim_size" delta="1"/> + <param name="infile1" value="train.tabular" ftype="tabular" /> + <param name="infile2" value="train.tabular" ftype="tabular" /> + <param name="header1" value="True" /> + <param name="header2" value="True" /> + <param name="col1" value="1,2,3,4" /> + <param name="col2" value="5" /> + <param name="selected_task" value="train" /> + <param name="selected_algorithm" value="LinearDiscriminantAnalysis" /> + <param name="solver" value="lsqr" /> + <output name="outfile_fit" file="lda_model02" compare="sim_size" delta="1" /> </test> <test> - <param name="infile1" value="train.tabular" ftype="tabular"/> - <param name="infile2" value="train.tabular" ftype="tabular"/> - <param name="header1" value="True"/> - <param name="header2" value="True"/> - <param name="col1" value="1,2,3,4"/> - <param name="col2" value="5"/> - <param name="selected_task" value="train"/> - <param name="selected_algorithm" value="QuadraticDiscriminantAnalysis"/> - <output name="outfile_fit" file="qda_model01" compare="sim_size" delta="1"/> + <param name="infile1" value="train.tabular" ftype="tabular" /> + <param name="infile2" value="train.tabular" ftype="tabular" /> + <param name="header1" value="True" /> + <param name="header2" value="True" /> + <param name="col1" value="1,2,3,4" /> + <param name="col2" value="5" /> + <param name="selected_task" value="train" /> + <param name="selected_algorithm" value="QuadraticDiscriminantAnalysis" /> + <output name="outfile_fit" file="qda_model01" compare="sim_size" delta="1" /> </test> <test> - <param name="infile_model" value="lda_model01" ftype="zip"/> - <param name="infile_data" value="test.tabular" ftype="tabular"/> - <param name="header" value="True"/> - <param name="selected_task" value="load"/> - <output name="outfile_predict" file="lda_prediction_result01.tabular"/> + <param name="infile_model" value="lda_model01" ftype="zip" /> + <param name="infile_data" value="test.tabular" ftype="tabular" /> + <param name="header" value="True" /> + <param name="selected_task" value="load" /> + <output name="outfile_predict" file="lda_prediction_result01.tabular" /> </test> <test> - <param name="infile_model" value="lda_model02" ftype="zip"/> - <param name="infile_data" value="test.tabular" ftype="tabular"/> - <param name="header" value="True"/> - <param name="selected_task" value="load"/> - <output name="outfile_predict" file="lda_prediction_result02.tabular"/> + <param name="infile_model" value="lda_model02" ftype="zip" /> + <param name="infile_data" value="test.tabular" ftype="tabular" /> + <param name="header" value="True" /> + <param name="selected_task" value="load" /> + <output name="outfile_predict" file="lda_prediction_result02.tabular" /> </test> <test> - <param name="infile_model" value="qda_model01" ftype="zip"/> - <param name="infile_data" value="test.tabular" ftype="tabular"/> - <param name="header" value="True"/> - <param name="selected_task" value="load"/> - <output name="outfile_predict" file="qda_prediction_result01.tabular"/> + <param name="infile_model" value="qda_model01" ftype="zip" /> + <param name="infile_data" value="test.tabular" ftype="tabular" /> + <param name="header" value="True" /> + <param name="selected_task" value="load" /> + <output name="outfile_predict" file="qda_prediction_result01.tabular" /> </test> </tests> <help><![CDATA[ @@ -208,6 +205,6 @@ .. _`Scikit-learn site`: http://scikit-learn.org/stable/modules/lda_qda.html - ]]></help> - <expand macro="sklearn_citation"/> + ]]> </help> + <expand macro="sklearn_citation" /> </tool>