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
line wrap: on
line diff
--- 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>