Previous changeset 4:681825b036f3 (2018-03-22) Next changeset 6:8fc64b67bb7f (2018-04-12) |
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 |
modified:
main_macros.xml |
added:
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 |
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diff -r 681825b036f3 -r c3b36f4c7e4e main_macros.xml --- a/main_macros.xml Thu Mar 22 13:46:32 2018 -0400 +++ b/main_macros.xml Tue Apr 10 15:18:33 2018 -0400 |
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@@ -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> |
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diff -r 681825b036f3 -r c3b36f4c7e4e test-data/gbc_model01 |
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Binary file test-data/gbc_model01 has changed |
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diff -r 681825b036f3 -r c3b36f4c7e4e test-data/gbc_result01 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gbc_result01 Tue Apr 10 15:18:33 2018 -0400 |
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@@ -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 |
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diff -r 681825b036f3 -r c3b36f4c7e4e test-data/gbr_model01 |
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Binary file test-data/gbr_model01 has changed |
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diff -r 681825b036f3 -r c3b36f4c7e4e test-data/gbr_prediction_result01.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gbr_prediction_result01.tabular Tue Apr 10 15:18:33 2018 -0400 |
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@@ -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 +2016 9 29 69 68 66.1 63 71 68 57 0 0 0 0 1 0 0 69.8047715468 +2016 4 27 59 60 60.7 59 65 60 50 0 0 0 0 0 0 1 62.3940847433 +2016 11 28 53 48 48.0 46 48 49 44 0 1 0 0 0 0 0 51.1656331745 +2016 10 12 60 62 61.0 60 63 63 52 0 0 0 0 0 0 1 60.7602326565 +2016 6 19 67 65 70.4 69 73 70 58 0 0 0 1 0 0 0 66.2416657667 +2016 5 7 68 77 63.0 61 65 63 83 0 0 1 0 0 0 0 71.7162060939 +2016 7 25 75 80 77.1 75 82 76 81 0 1 0 0 0 0 0 78.6168727393 +2016 8 15 90 83 76.6 76 79 75 70 0 1 0 0 0 0 0 77.9015583717 +2016 10 28 58 60 55.6 52 56 55 52 1 0 0 0 0 0 0 61.4191796096 +2016 6 5 80 81 68.0 64 70 66 54 0 0 0 1 0 0 0 74.4136969328 +2016 3 19 58 63 54.2 54 59 54 62 0 0 1 0 0 0 0 60.9589968112 +2016 6 7 92 86 68.3 67 69 70 58 0 0 0 0 0 1 0 75.5031094008 +2016 12 10 41 36 45.9 44 48 44 65 0 0 1 0 0 0 0 38.5555100028 +2016 4 23 73 64 59.9 56 63 59 57 0 0 1 0 0 0 0 64.0035135524 +2016 6 24 75 68 71.5 67 73 73 65 1 0 0 0 0 0 0 74.5305649268 +2016 2 9 51 57 49.4 45 52 49 57 0 0 0 0 0 1 0 57.0110982119 +2016 11 10 71 65 52.2 52 54 51 38 0 0 0 0 1 0 0 61.876179905 +2016 3 21 61 55 54.5 52 56 55 52 0 1 0 0 0 0 0 56.0732986026 +2016 2 28 60 57 51.3 48 56 53 66 0 0 0 1 0 0 0 56.9672058242 +2016 6 28 78 85 72.4 72 76 74 67 0 0 0 0 0 1 0 78.4438620045 +2016 10 6 63 66 63.3 62 67 63 55 0 0 0 0 1 0 0 63.9639842609 +2016 2 17 55 56 50.0 45 51 49 46 0 0 0 0 0 0 1 54.149464399 +2016 6 15 66 60 69.7 65 73 71 69 0 0 0 0 0 0 1 66.1043951877 +2016 10 15 60 60 59.9 59 62 59 46 0 0 1 0 0 0 0 61.6791270097 +2016 3 26 54 57 55.2 53 57 55 54 0 0 1 0 0 0 0 60.2367595132 +2016 1 26 51 54 48.3 44 53 50 61 0 0 0 0 0 1 0 52.9547372573 +2016 5 23 59 66 66.1 63 68 68 66 0 1 0 0 0 0 0 64.6813560623 +2016 1 10 48 50 46.5 45 48 48 49 0 0 0 1 0 0 0 45.1415524342 +2016 5 22 66 59 65.9 62 66 65 80 0 0 0 1 0 0 0 59.8874932366 +2016 7 15 75 77 76.0 74 80 78 75 1 0 0 0 0 0 0 82.9044308458 +2016 4 22 81 73 59.7 59 64 60 59 1 0 0 0 0 0 0 74.8537745899 +2016 4 29 61 64 61.2 61 65 61 49 1 0 0 0 0 0 0 65.3872817114 +2016 1 23 52 57 48.0 45 49 50 37 0 0 1 0 0 0 0 51.8565179701 +2016 8 16 83 84 76.5 72 78 78 90 0 0 0 0 0 1 0 83.6982049493 +2016 8 1 76 73 77.4 76 78 79 65 0 1 0 0 0 0 0 72.4140203449 +2016 2 27 61 60 51.2 51 53 53 61 0 0 1 0 0 0 0 60.839700499 +2016 2 12 56 55 49.6 49 52 48 33 1 0 0 0 0 0 0 54.9702164699 +2016 1 31 52 48 48.7 47 52 49 61 0 0 0 1 0 0 0 49.8435633428 +2016 9 5 67 68 73.5 71 75 73 54 0 1 0 0 0 0 0 69.325684558 +2016 12 20 39 46 45.1 45 49 45 62 0 0 0 0 0 1 0 43.4575487159 +2016 5 1 61 68 61.6 60 65 60 75 0 0 0 1 0 0 0 65.0535826144 +2016 3 28 59 51 55.5 55 57 55 47 0 1 0 0 0 0 0 57.5541221212 +2016 4 21 81 81 59.4 55 61 59 55 0 0 0 0 1 0 0 76.9948007001 +2016 1 6 40 44 46.1 43 49 48 40 0 0 0 0 0 0 1 41.3862075834 +2016 10 21 58 62 57.8 56 60 59 44 1 0 0 0 0 0 0 61.0523769432 +2016 5 2 68 77 61.9 60 66 61 59 0 1 0 0 0 0 0 74.2435105222 +2016 3 1 53 54 51.5 48 56 50 53 0 0 0 0 0 1 0 54.3306325137 +2016 7 21 78 82 76.8 73 81 78 84 0 0 0 0 1 0 0 81.2097724662 +2016 3 17 51 53 53.9 49 58 52 62 0 0 0 0 1 0 0 52.1836048796 +2016 12 6 46 40 46.4 44 50 45 56 0 0 0 0 0 1 0 42.2019357209 +2016 12 21 46 51 45.1 44 50 46 39 0 0 0 0 0 0 1 45.9011800782 +2016 1 4 44 41 45.9 44 48 46 53 0 1 0 0 0 0 0 41.1820761074 +2016 10 2 67 63 64.9 62 69 66 82 0 0 0 1 0 0 0 61.3727414202 +2016 5 28 65 64 66.8 64 69 65 64 0 0 1 0 0 0 0 65.5895934942 +2016 9 11 74 77 72.1 69 75 71 70 0 0 0 1 0 0 0 74.3381013887 +2016 10 25 62 61 56.5 53 60 55 70 0 0 0 0 0 1 0 61.2657495686 +2016 2 18 56 57 50.1 47 55 49 34 0 0 0 0 1 0 0 55.5571516621 +2016 11 1 117 59 54.5 51 59 55 61 0 0 0 0 0 1 0 60.8285501381 +2016 3 16 49 51 53.7 52 54 55 65 0 0 0 0 0 0 1 54.4944109202 +2016 4 26 55 59 60.5 56 61 62 75 0 0 0 0 0 1 0 61.8372077373 +2016 6 10 67 65 68.8 67 71 67 73 1 0 0 0 0 0 0 63.9222528587 +2016 2 3 46 51 48.9 48 49 50 40 0 0 0 0 0 0 1 48.8811572638 +2016 3 7 64 60 52.4 49 57 53 71 0 1 0 0 0 0 0 62.8822601273 +2016 9 18 75 68 70.0 66 73 71 90 0 0 0 1 0 0 0 71.4706106408 +2016 3 20 63 61 54.3 51 56 55 50 0 0 0 1 0 0 0 59.7324860951 +2016 4 6 60 57 56.8 53 59 57 64 0 0 0 0 0 0 1 58.9890626595 +2016 7 2 73 76 73.3 70 77 73 84 0 0 1 0 0 0 0 71.2799971324 +2016 7 5 71 68 74.0 72 77 74 62 0 0 0 0 0 1 0 68.9560415136 +2016 7 19 80 73 76.6 76 78 77 90 0 0 0 0 0 1 0 77.0157028161 +2016 12 9 40 41 46.0 43 51 44 54 1 0 0 0 0 0 0 42.1221149466 +2016 6 29 85 79 72.6 68 76 74 81 0 0 0 0 0 0 1 74.3021609896 +2016 3 22 55 56 54.6 51 55 54 64 0 0 0 0 0 1 0 57.100481947 +2016 4 3 71 63 56.3 54 61 56 64 0 0 0 1 0 0 0 60.29402298 +2016 1 17 48 54 47.4 45 51 46 47 0 0 0 1 0 0 0 50.2034551756 +2016 3 10 54 55 52.8 49 55 53 50 0 0 0 0 1 0 0 55.1100177804 +2016 5 9 82 63 63.4 59 66 62 64 0 1 0 0 0 0 0 61.9408775418 +2016 1 8 51 45 46.3 43 47 46 34 1 0 0 0 0 0 0 45.3158658848 +2016 8 11 72 76 76.9 74 81 75 80 0 0 0 0 1 0 0 74.2995087324 +2016 12 29 47 48 45.3 43 50 45 65 0 0 0 0 1 0 0 47.8575821187 +2016 11 23 54 54 49.1 48 52 49 38 0 0 0 0 0 0 1 51.5257711552 +2016 11 19 52 55 50.0 50 54 49 56 0 0 1 0 0 0 0 53.6344142464 +2016 4 7 57 68 56.9 52 61 55 38 0 0 0 0 1 0 0 66.7238759737 +2016 6 4 71 80 67.9 63 72 66 76 0 0 1 0 0 0 0 72.7073855763 +2016 6 17 67 71 70.0 66 74 69 54 1 0 0 0 0 0 0 73.4041601901 +2016 10 5 61 63 63.7 61 66 65 48 0 0 0 0 0 0 1 63.9616628787 +2016 3 4 55 59 51.9 47 56 53 45 1 0 0 0 0 0 0 58.3547591361 +2016 12 22 51 49 45.1 42 47 46 38 0 0 0 0 1 0 0 44.7834274452 |
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diff -r 681825b036f3 -r c3b36f4c7e4e test-data/regression_X.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/regression_X.tabular Tue Apr 10 15:18:33 2018 -0400 |
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|
b |
diff -r 681825b036f3 -r c3b36f4c7e4e test-data/regression_test_X.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/regression_test_X.tabular Tue Apr 10 15:18:33 2018 -0400 |
b |
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b |
diff -r 681825b036f3 -r c3b36f4c7e4e test-data/regression_y.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/regression_y.tabular Tue Apr 10 15:18:33 2018 -0400 |
b |
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