Mercurial > repos > bgruening > sklearn_svm_classifier
diff svm.xml @ 19:d67dcd63f6cb draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author | bgruening |
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date | Tue, 13 Apr 2021 17:32:55 +0000 |
parents | 2df8f5c30edc |
children | b878e4cdd63a |
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--- a/svm.xml Thu Oct 01 20:06:56 2020 +0000 +++ b/svm.xml Tue Apr 13 17:32:55 2021 +0000 @@ -1,20 +1,20 @@ -<tool id="sklearn_svm_classifier" name="Support vector machines (SVMs)" version="@VERSION@"> +<tool id="sklearn_svm_classifier" name="Support vector machines (SVMs)" version="@VERSION@" profile="20.05"> <description>for classification</description> <macros> <import>main_macros.xml</import> <!-- macro name="class_weight" argument="class_weight"--> </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 '$svc_script' '$inputs' ]]> </command> <configfiles> - <inputs name="inputs"/> + <inputs name="inputs" /> <configfile name="svc_script"> -<![CDATA[ + <![CDATA[ import sys import json import sklearn.svm @@ -72,110 +72,110 @@ <option value="LinearSVC">Linear Support Vector Classification</option> </param> <when value="SVC"> - <expand macro="sl_mixed_input"/> + <expand macro="sl_mixed_input" /> <expand macro="svc_advanced_options"> - <expand macro="C"/> + <expand macro="C" /> </expand> </when> <when value="NuSVC"> - <expand macro="sl_mixed_input"/> + <expand macro="sl_mixed_input" /> <expand macro="svc_advanced_options"> - <param argument="nu" type="float" optional="true" value="0.5" label="Nu control parameter" help="Controls the number of support vectors. Should be in the interval (0, 1]. "/> + <param argument="nu" type="float" optional="true" value="0.5" label="Nu control parameter" help="Controls the number of support vectors. Should be in the interval (0, 1]. " /> </expand> </when> <when value="LinearSVC"> - <expand macro="sl_mixed_input"/> + <expand macro="sl_mixed_input" /> <section name="options" title="Advanced Options" expanded="False"> - <expand macro="C"/> - <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/> - <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results."/> + <expand macro="C" /> + <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. " /> + <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results." /> <!--expand macro="class_weight"/--> - <param argument="max_iter" type="integer" optional="true" value="1000" label="Maximum number of iterations" help="The maximum number of iterations to be run."/> + <param argument="max_iter" type="integer" optional="true" value="1000" label="Maximum number of iterations" help="The maximum number of iterations to be run." /> <param argument="loss" type="select" label="Loss function" help="Specifies the loss function. ''squared_hinge'' is the square of the hinge loss."> <option value="squared_hinge" selected="true">Squared hinge</option> <option value="hinge">Hinge</option> </param> <param argument="penalty" type="select" label="Penalization norm" help=" "> - <option value="l1" >l1</option> + <option value="l1">l1</option> <option value="l2" selected="true">l2</option> </param> - <param argument="dual" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use the shrinking heuristic" help="Select the algorithm to either solve the dual or primal optimization problem. Prefer dual=False when n_samples > n_features."/> + <param argument="dual" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use the shrinking heuristic" help="Select the algorithm to either solve the dual or primal optimization problem. Prefer dual=False when n_samples > n_features." /> <param argument="multi_class" type="select" label="Multi-class strategy" help="Determines the multi-class strategy if y contains more than two classes."> <option value="ovr" selected="true">ovr</option> - <option value="crammer_singer" >crammer_singer</option> + <option value="crammer_singer">crammer_singer</option> </param> - <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Calculate the intercept for this model" help="If set to false, data is expected to be already centered."/> - <param argument="intercept_scaling" type="float" optional="true" value="1" label="Add synthetic feature to the instance vector" help=" "/> + <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Calculate the intercept for this model" help="If set to false, data is expected to be already centered." /> + <param argument="intercept_scaling" type="float" optional="true" value="1" label="Add synthetic feature to the instance vector" help=" " /> </section> </when> </expand> </inputs> - <expand macro="output"/> + <expand macro="output" /> <tests> <test> - <param name="infile1" value="train_set.tabular" ftype="tabular"/> - <param name="infile2" value="train_set.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="SVC"/> - <param name="random_state" value="5"/> - <output name="outfile_fit" file="svc_model01" compare="sim_size"/> + <param name="infile1" value="train_set.tabular" ftype="tabular" /> + <param name="infile2" value="train_set.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="SVC" /> + <param name="random_state" value="5" /> + <output name="outfile_fit" file="svc_model01" compare="sim_size" /> </test> <test> - <param name="infile1" value="train_set.tabular" ftype="tabular"/> - <param name="infile2" value="train_set.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="NuSVC"/> - <param name="random_state" value="5"/> - <output name="outfile_fit" file="svc_model02" compare="sim_size"/> + <param name="infile1" value="train_set.tabular" ftype="tabular" /> + <param name="infile2" value="train_set.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="NuSVC" /> + <param name="random_state" value="5" /> + <output name="outfile_fit" file="svc_model02" compare="sim_size" /> </test> <test> - <param name="infile1" value="train_set.tabular" ftype="tabular"/> - <param name="infile2" value="train_set.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="LinearSVC"/> - <param name="random_state" value="5"/> - <output name="outfile_fit" file="svc_model03" compare="sim_size"/> + <param name="infile1" value="train_set.tabular" ftype="tabular" /> + <param name="infile2" value="train_set.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="LinearSVC" /> + <param name="random_state" value="5" /> + <output name="outfile_fit" file="svc_model03" compare="sim_size" /> </test> <test> - <param name="infile_model" value="svc_model01" ftype="zip"/> - <param name="infile_data" value="test_set.tabular" ftype="tabular"/> - <param name="header" value="True"/> - <param name="selected_task" value="load"/> - <output name="outfile_predict" file="svc_prediction_result01.tabular"/> + <param name="infile_model" value="svc_model01" ftype="zip" /> + <param name="infile_data" value="test_set.tabular" ftype="tabular" /> + <param name="header" value="True" /> + <param name="selected_task" value="load" /> + <output name="outfile_predict" file="svc_prediction_result01.tabular" /> </test> <test> - <param name="infile_model" value="svc_model02" ftype="zip"/> - <param name="infile_data" value="test_set.tabular" ftype="tabular"/> - <param name="header" value="True"/> - <param name="selected_task" value="load"/> - <output name="outfile_predict" file="svc_prediction_result02.tabular"/> + <param name="infile_model" value="svc_model02" ftype="zip" /> + <param name="infile_data" value="test_set.tabular" ftype="tabular" /> + <param name="header" value="True" /> + <param name="selected_task" value="load" /> + <output name="outfile_predict" file="svc_prediction_result02.tabular" /> </test> <test> - <param name="infile_model" value="svc_model03" ftype="zip"/> - <param name="infile_data" value="test_set.tabular" ftype="tabular"/> - <param name="header" value="True"/> - <param name="selected_task" value="load"/> - <output name="outfile_predict" file="svc_prediction_result03.tabular"/> + <param name="infile_model" value="svc_model03" ftype="zip" /> + <param name="infile_data" value="test_set.tabular" ftype="tabular" /> + <param name="header" value="True" /> + <param name="selected_task" value="load" /> + <output name="outfile_predict" file="svc_prediction_result03.tabular" /> </test> <!-- The following test is expected to fail, it is testing the whitelist/blacklist filtering. It loads a pickle with malicious content that we do not accept. --> <test expect_failure="true"> - <param name="infile_model" value="pickle_blacklist" ftype="zip"/> - <param name="infile_data" value="test_set.tabular" ftype="tabular"/> - <param name="header" value="True"/> - <param name="selected_task" value="load"/> + <param name="infile_model" value="pickle_blacklist" ftype="zip" /> + <param name="infile_data" value="test_set.tabular" ftype="tabular" /> + <param name="header" value="True" /> + <param name="selected_task" value="load" /> </test> </tests> <help><![CDATA[ @@ -203,5 +203,5 @@ ]]> </help> - <expand macro="sklearn_citation"/> + <expand macro="sklearn_citation" /> </tool>