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changeset 5:06b71e58a943 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
author bgruening
date Tue, 10 Apr 2018 15:18:18 -0400
parents d2f23b211af8
children 9eecaf90aeb6
files main_macros.xml test-data/gbc_model01 test-data/gbc_result01 test-data/gbr_model01 test-data/gbr_prediction_result01.tabular test-data/regression_X.tabular test-data/regression_test_X.tabular test-data/regression_y.tabular
diffstat 8 files changed, 760 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/main_macros.xml	Thu Mar 22 13:46:16 2018 -0400
+++ b/main_macros.xml	Tue Apr 10 15:18:18 2018 -0400
@@ -66,6 +66,7 @@
         <when value="load">
             <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
             <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
+            <param name="header" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
             <conditional name="prediction_options">
                 <param name="prediction_option" type="select" label="Select the type of prediction">
                     <option value="predict">Predict class labels</option>
@@ -174,12 +175,12 @@
     <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
   </xml>
 
-  <xml name="min_samples_split" token_default_value="2" token_help=" ">
-    <param argument="min_samples_split" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples required to split an internal node" help="@HELP@"/>
+  <xml name="min_samples_split" token_type="integer" token_default_value="2" token_help=" ">
+    <param argument="min_samples_split" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples required to split an internal node" help="@HELP@"/>
   </xml>
 
-  <xml name="min_samples_leaf" token_default_value="1" token_help=" ">
-    <param argument="min_samples_leaf" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples in newly created leaves" help="@HELP@"/>
+  <xml name="min_samples_leaf" token_type="integer" token_default_value="1" token_label="Minimum number of samples in newly created leaves" token_help=" ">
+    <param argument="min_samples_leaf" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP@"/>
   </xml>
 
   <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
@@ -190,6 +191,10 @@
     <param argument="max_leaf_nodes" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum number of leaf nodes in best-first method" help="@HELP@"/>
   </xml>
 
+  <xml name="min_impurity_decrease" token_default_value="0" token_help=" ">
+    <param argument="min_impurity_decrease" type="float" value="@DEFAULT_VALUE@" optional="true" label="The threshold value of impurity for stopping node splitting" help="@HELP@"/>
+  </xml>
+
   <xml name="bootstrap" token_checked="true" token_help=" ">
     <param argument="bootstrap" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use bootstrap samples for building trees." help="@HELP@"/>
   </xml>
@@ -202,18 +207,57 @@
     </param>
   </xml>
 
+  <xml name="criterion2" token_help="">
+    <param argument="criterion" type="select" label="Function to measure the quality of a split" >
+      <option value="mse">mse - mean squared error</option>
+      <option value="mae">mae - mean absolute error</option>
+      <yield/>
+    </param>
+  </xml>
+
   <xml name="oob_score" token_checked="false" token_help=" ">
     <param argument="oob_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use out-of-bag samples to estimate the generalization error" help="@HELP@"/>
   </xml>
 
-  <xml name="max_features" token_default_value="auto" token_help="This could be an integer, float, string, or None. For more information please refer to help. ">
-    <param argument="max_features" type="text" optional="true" value="@DEFAULT_VALUE@" label="Number of features for finding the best split" help="@HELP@"/>
+  <xml name="max_features">
+    <conditional name="select_max_features">
+      <param argument="max_features" type="select" label="max_features">
+        <option value="auto" selected="true">auto - max_features=n_features</option>
+        <option value="sqrt">sqrt - max_features=sqrt(n_features)</option>
+        <option value="log2">log2 - max_features=log2(n_features)</option>
+        <option value="number_input">I want to type the number in or input None type</option>
+      </param>
+      <when value="auto">
+      </when>
+      <when value="sqrt">
+      </when>
+      <when value="log2">
+      </when>
+      <when value="number_input">
+        <param name="num_max_features" type="float" value="" optional="true" label="Input max_features number:" help="If int, consider the number of features at each split; If float, then max_features is a percentage and int(max_features * n_features) features are considered at each split."/>
+      </when>
+    </conditional>
+  </xml>
+
+  <xml name="verbose" token_default_value="0" token_help="If 1 then it prints progress and performance once in a while. If greater than 1 then it prints progress and performance for every tree.">
+    <param argument="verbose" type="integer" value="@DEFAULT_VALUE@" optional="true" label="Enable verbose output" help="@HELP@"/>
   </xml>
 
   <xml name="learning_rate" token_default_value="1.0" token_help=" ">
     <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/>
   </xml>
 
+  <xml name="subsample" token_help=" ">
+    <param argument="subsample" type="float" value="1.0" optional="true" label="The fraction of samples to be used for fitting the individual base learners" help="@HELP@"/>
+  </xml>
+
+  <xml name="presort">
+    <param argument="presort" type="select" label="Whether to presort the data to speed up the finding of best splits in fitting" >
+      <option value="auto" selected="true">auto</option>
+      <option value="true">true</option>
+      <option value="false">false</option>
+    </param>
+  </xml>
 
   <!--Parameters-->
   <xml name="tol" token_default_value="0.0" token_help_text="Early stopping heuristics based on the relative center changes. Set to default (0.0) to disable this convergence detection.">
@@ -228,6 +272,10 @@
     <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered."/>
   </xml>
 
+  <xml name="n_jobs" token_default_value="1" token_label="The number of jobs to run in parallel for both fit and predict">
+    <param argument="n_jobs" type="integer" value="@DEFAULT_VALUE@" optional="true" label="@LABEL@" help="If -1, then the number of jobs is set to the number of cores"/>
+  </xml>
+
   <xml name="n_iter" token_default_value="5" token_help_text="The number of passes over the training data (aka epochs). ">
     <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
   </xml>
Binary file test-data/gbc_model01 has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gbc_result01	Tue Apr 10 15:18:18 2018 -0400
@@ -0,0 +1,6 @@
+0	1	2	3	0
+3.68258022948	2.82110345641	-3.990140724	-1.9523364774	1
+0.015942057224	-0.711958594347	0.125502976978	-0.972218263337	0
+2.08690768825	0.929399321468	-2.12924084484	-1.99714022188	1
+1.41321052084	0.523750660422	-1.4210539291	-1.49298569451	1
+0.76831404394	1.38267855169	-0.989045048734	0.649504257894	1
Binary file test-data/gbr_model01 has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gbr_prediction_result01.tabular	Tue Apr 10 15:18:18 2018 -0400
@@ -0,0 +1,88 @@
+year	month	day	temp_2	temp_1	average	forecast_noaa	forecast_acc	forecast_under	friend	week_Fri	week_Mon	week_Sat	week_Sun	week_Thurs	week_Tues	week_Wed	0
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/regression_X.tabular	Tue Apr 10 15:18:18 2018 -0400
@@ -0,0 +1,262 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/regression_test_X.tabular	Tue Apr 10 15:18:18 2018 -0400
@@ -0,0 +1,88 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/regression_y.tabular	Tue Apr 10 15:18:18 2018 -0400
@@ -0,0 +1,262 @@
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