Mercurial > repos > jay > pdaug_ml_models
diff PDAUG_ML_Models/PDAUG_ML_Models.xml @ 0:0973f093d98f draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
| author | jay |
|---|---|
| date | Wed, 28 Oct 2020 02:31:40 +0000 |
| parents | |
| children | 5448f9425c6a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_ML_Models/PDAUG_ML_Models.xml Wed Oct 28 02:31:40 2020 +0000 @@ -0,0 +1,761 @@ +<tool id="pdaug_ml_models" name="PDAUG ML Models" version="0.1.0" python_template_version="3.6"> + <description> Machine learning modeling </description> + + <requirements> + + <requirement type="package" version="4.10.0">plotly</requirement> + <requirement type="package" version="3.6">python</requirement> + <requirement type="package" version="0.25.3">pandas</requirement> + <requirement type="package" version="0.22.1">scikit-learn</requirement> + <requirement type="package" version="1.5.2">scipy</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ + + python '$__tool_directory__/PDAUG_ML_Models.py' '$SelMLAlgo.MLAlgo' + + #if $SelMLAlgo.MLAlgo == 'SVMC' + #if $SelMLAlgo.settings.advanced == "advanced" + --cache_size $SelMLAlgo.settings.cache_size + --C $SelMLAlgo.settings.C + --kernel '$SelMLAlgo.settings.kernel' + --degree '$SelMLAlgo.settings.degree' + --gamma '$SelMLAlgo.settings.gamma' + --coef0 '$SelMLAlgo.settings.coef0' + --probability '$SelMLAlgo.settings.probability' + --shrinking '$SelMLAlgo.settings.shrinking' + --tol '$SelMLAlgo.settings.tol' + --verbose '$SelMLAlgo.settings.verbose' + --max_iter '$SelMLAlgo.settings.max_iter' + --decision_function_shape '$SelMLAlgo.settings.decision_function_shape' + --randomState '$SelMLAlgo.settings.randomState' + --breakties '$SelMLAlgo.settings.breakties' + #end if + #end if + + #if $SelMLAlgo.MLAlgo == 'SGDC' + #if $SelMLAlgo.settings.advanced == "advanced" + --loss $SelMLAlgo.settings.loss + --penalty $SelMLAlgo.settings.penalty + --alpha $SelMLAlgo.settings.alpha + --l1_ratio $SelMLAlgo.settings.l1_ratio + --fit_intercept $SelMLAlgo.settings.fit_intercept + --max_iter $SelMLAlgo.settings.max_iter + --tol $SelMLAlgo.settings.tol + --shuffle $SelMLAlgo.settings.shuffle + --verbose $SelMLAlgo.settings.verbose + --epsilon $SelMLAlgo.settings.epsilon + --n_jobs $SelMLAlgo.settings.n_jobs + --random_state $SelMLAlgo.settings.random_state + --learning_rate $SelMLAlgo.settings.learning_rate + --eta0 $SelMLAlgo.settings.eta0 + --power_t $SelMLAlgo.settings.power_t + --early_stopping $SelMLAlgo.settings.early_stopping + --validation_fraction $SelMLAlgo.settings.validation_fraction + --n_iter_no_change $SelMLAlgo.settings.n_iter_no_change + --warm_start $SelMLAlgo.settings.warm_start + --average $SelMLAlgo.settings.average + + #end if + #end if + + #if $SelMLAlgo.MLAlgo == 'DTC' + #if $SelMLAlgo.settings.advanced == "advanced" + --criterion $SelMLAlgo.settings.criterion + --splitter $SelMLAlgo.settings.splitter + --max_depth $SelMLAlgo.settings.max_depth + --min_samples_split $SelMLAlgo.settings.min_samples_split + --min_samples_leaf $SelMLAlgo.settings.min_samples_leaf + --min_weight_fraction_leaf $SelMLAlgo.settings.min_weight_fraction_leaf + --max_features $SelMLAlgo.settings.max_features + --random_state $SelMLAlgo.settings.random_state + --max_leaf_nodes $SelMLAlgo.settings.max_leaf_nodes + --min_impurity_decrease $SelMLAlgo.settings.min_impurity_decrease + --min_impurity_split $SelMLAlgo.settings.min_impurity_split + --presort $SelMLAlgo.settings.presort + --ccpalpha $SelMLAlgo.settings.ccpalpha + #end if + #end if + + + #if $SelMLAlgo.MLAlgo == 'GBC' + #if $SelMLAlgo.settings.advanced == "advanced" + --loss $SelMLAlgo.settings.loss + --learning_rate $SelMLAlgo.settings.learning_rate + --n_estimators $SelMLAlgo.settings.n_estimators + --subsample $SelMLAlgo.settings.subsample + --criterion $SelMLAlgo.settings.criterion + --min_samples_split $SelMLAlgo.settings.min_samples_split + --min_samples_leaf $SelMLAlgo.settings.min_samples_leaf + --min_weight_fraction_leaf $SelMLAlgo.settings.min_weight_fraction_leaf + --max_depth $SelMLAlgo.settings.max_depth + --min_impurity_decrease $SelMLAlgo.settings.min_impurity_decrease + --min_impurity_split $SelMLAlgo.settings.min_impurity_split + --init $SelMLAlgo.settings.init + --random_state $SelMLAlgo.settings.random_state + --max_features $SelMLAlgo.settings.max_features + --verbose $SelMLAlgo.settings.verbose + --max_leaf_nodes $SelMLAlgo.settings.max_leaf_nodes + --warm_start $SelMLAlgo.settings.warm_start + --presort $SelMLAlgo.settings.presort + --validation_fraction $SelMLAlgo.settings.validation_fraction + --n_iter_no_change $SelMLAlgo.settings.n_iter_no_change + --tol $SelMLAlgo.settings.tol + --ccpalpha $SelMLAlgo.settings.ccpalpha + #end if + #end if + + #if $SelMLAlgo.MLAlgo == 'RFC' + #if $SelMLAlgo.settings.advanced == "advanced" + --n_estimators $SelMLAlgo.settings.n_estimators + --criterion $SelMLAlgo.settings.criterion + --max_depth $SelMLAlgo.settings.max_depth + --min_samples_split $SelMLAlgo.settings.min_samples_split + --min_samples_leaf $SelMLAlgo.settings.min_samples_leaf + --min_weight_fraction_leaf $SelMLAlgo.settings.min_weight_fraction_leaf + --max_features $SelMLAlgo.settings.max_features + --max_leaf_nodes $SelMLAlgo.settings.max_leaf_nodes + --min_impurity_decrease $SelMLAlgo.settings.min_impurity_decrease + --min_impurity_split $SelMLAlgo.settings.min_impurity_split + --bootstrap $SelMLAlgo.settings.bootstrap + --oob_score $SelMLAlgo.settings.oob_score + --n_jobs $SelMLAlgo.settings.n_jobs + --random_state $SelMLAlgo.settings.random_state + --verbose $SelMLAlgo.settings.verbose + --warm_start $SelMLAlgo.settings.warm_start + --ccp_alpha $SelMLAlgo.settings.ccp_alpha + --max_samples $SelMLAlgo.settings.max_samples + #end if + #end if + + + #if $SelMLAlgo.MLAlgo == 'LRC' + #if $SelMLAlgo.settings.advanced == "advanced" + --penalty $SelMLAlgo.settings.penalty + --dual $SelMLAlgo.settings.dual + --tol $SelMLAlgo.settings.tol + --C $SelMLAlgo.settings.C + --fit_intercept $SelMLAlgo.settings.fit_intercept + --intercept_scaling $SelMLAlgo.settings.intercept_scaling + --random_state $SelMLAlgo.settings.random_state + --solver $SelMLAlgo.settings.solver + --max_iter $SelMLAlgo.settings.max_iter + --multi_class $SelMLAlgo.settings.multi_class + --verbose $SelMLAlgo.settings.verbose + --warm_start $SelMLAlgo.settings.warm_start + --n_jobs $SelMLAlgo.settings.n_jobs + --l1_ratio $SelMLAlgo.settings.l1_ratio + #end if + #end if + + #if $SelMLAlgo.MLAlgo == 'KNC' + #if $SelMLAlgo.settings.advanced == "advanced" + --n_neighbors $SelMLAlgo.settings.n_neighbors + --weights $SelMLAlgo.settings.weights + --algorithm $SelMLAlgo.settings.algorithm + --leaf_size $SelMLAlgo.settings.leaf_size + --p $SelMLAlgo.settings.p + --metric $SelMLAlgo.settings.metric + --n_jobs $SelMLAlgo.settings.n_jobs + #end if + #end if + + #if $SelMLAlgo.MLAlgo == 'GNBC' + #if $SelMLAlgo.settings.advanced == "advanced" + --var_smoothing $SelMLAlgo.settings.var_smoothing + #end if + #end if + + #if $SelMLAlgo.MLAlgo == 'MLP' + #if $SelMLAlgo.settings.advanced == "advanced" + --hidden_layer_sizes $SelMLAlgo.settings.hidden_layer_sizes + --activation $SelMLAlgo.settings.activation + --solver $SelMLAlgo.settings.solver + --alpha $SelMLAlgo.settings.alpha + --batch_size $SelMLAlgo.settings.batch_size + --learning_rate $SelMLAlgo.settings.learning_rate + --learning_rate_init $SelMLAlgo.settings.learning_rate_init + --power_t $SelMLAlgo.settings.power_t + --max_iter $SelMLAlgo.settings.max_iter + --shuffle $SelMLAlgo.settings.shuffle + --random_state $SelMLAlgo.settings.random_state + --tol $SelMLAlgo.settings.tol + --verbose $SelMLAlgo.settings.verbose + --warm_start $SelMLAlgo.settings.warm_start + --momentum $SelMLAlgo.settings.momentum + --nesterovs_momentum $SelMLAlgo.settings.nesterovs_momentum + --early_stopping $SelMLAlgo.settings.early_stopping + --validation_fraction $SelMLAlgo.settings.validation_fraction + --beta_1 $SelMLAlgo.settings.beta_1 + --beta_2 $SelMLAlgo.settings.beta_2 + --epsilon $SelMLAlgo.settings.epsilon + --n_iter_no_change $SelMLAlgo.settings.n_iter_no_change + --max_fun $SelMLAlgo.settings.max_fun + --TrainFile $SelMLAlgo.settings.TrainFile + --TestMethod $SelMLAlgo.settings.TestMethod + --SelectedSclaer $SelMLAlgo.settings.SelectedSclaer + --NFolds $SelMLAlgo.settings.NFolds + --Testspt $SelMLAlgo.settings.Testspt + --TestFile $SelMLAlgo.settings.TestFile + --OutFile $SelMLAlgo.settings.OutFile + --htmlOutDir $SelMLAlgo.settings.htmlOutDir + --htmlFname $SelMLAlgo.settings.htmlFname + --Workdirpath $SelMLAlgo.settings.Workdirpath + #end if + #end if + + --TrainFile '$input1' --TestMethod '$TestMethods.SelTestMethods' --SelectedSclaer '$scalling' + --htmlOutDir '$output2.extra_files_path' + + --htmlFname '$output2' + + --OutFile '$output1' + + #if $TestMethods.SelTestMethods == 'predict' + --TestFile '$TestMethods.input2' + #end if + + #if $TestMethods.SelTestMethods == 'Internal' + --NFolds '$TestMethods.nFolds' + #end if + ]]></command> + + <inputs> + + <param name="input1" label="Input file" type="data" format="tabular" argument= "--TrainFile"/> + + <conditional name='SelMLAlgo' > + + <param name="MLAlgo" type="select" label="Machine learning algorithms" argument=""> + <option value="SVMC">SVMC</option> + <option value="SGDC">SGDC</option> + <option value="DTC">DTC</option> + <option value="GBC">GBC</option> + <option value="RFC">RFC</option> + <option value="LRC">LRC</option> + <option value="KNC">KNC</option> + <option value="GNBC">GNBC</option> + <option value="MLP">MLP</option> + </param> + + <when value="SVMC"> + <conditional name="settings"> + <param name="advanced" type="select" label="Select advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + <when value="simple"> + + </when> + + <when value="advanced"> + <param name="C" type="float" label="Regularization parameter" value="1.0" help="Regularization parameter. For details(https://scikit-learn.org/stable/modules/generated/sklearn.svm.SVC.html)" argument="--C"/> + <param name="kernel" type="select" label="Kernel" argument="" help="Specifies the kernel type to be used in the algorithm."> + <option value="rbf">rbf</option> + <option value="poly">poly</option> + <option value="linear">linear</option> + <option value="sigmoid">sigmoid </option> + </param> + <param name="degree" type="integer" label="degree" value="3" help="degree" /> + <param name="gamma" type="text" label="gamma" value="scale" help="gamma" /> + <param name="coef0" type="float" label="coef0" value="0.0" help="coef0" /> + <param name="shrinking" type="boolean" label="shrinking" value="true" help="shrinking" /> + <param name="probability" type="boolean" label="probability" value="true" help="probability" /> + <param name="tol" type="float" label="tol" value="1e-3" help="tol" /> + <param name="verbose" type="boolean" label="verbose" value="false" help="verbose" /> + <param name="max_iter" type="integer" label="max_iter" value="-1" help="max_iter" /> + <param name="decision_function_shape" type="select" label="decision_function_shape" argument="" help="Decision Function Shape"> + <option value="ovo">ovo</option> + <option value="ovr">ovr</option> + </param> + <param name="randomState" type="integer" label="randomState" value="100" help="Random State)" /> + <param name="breakties" type="boolean" label="breakties" value="false" help="Break ties" /> + <param name="cache_size" type="float" label="cache_size" value="100" help="Cache size" /> + </when> + </conditional> + </when> + + <when value="SGDC"> + <conditional name="settings"> + <param name="advanced" type="select" label="Specify advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + <when value="simple"> + </when> + + <when value="advanced"> + <param name="loss" type="select" label="loss" argument="" help="--loss" > + <option value="hinge" > hinge</option> + <option value="log" selected="true" > log </option> + <option value="modified_huber" > modified_huber </option> + <option value="squared_hinger" > squared_hinger </option> + <option value="perceptron" > perceptron </option> + </param> + <param name="penalty" type="select" label="penalty" argument="" help="--penalty" > + <option value="l2" selected="true"> l2 </option> + <option value="l1"> l1 </option> + <option value="elasticnet" > elasticnet </option> + </param> + <param name="alpha" type="float" label="alpha" value="0.0001" help="--alpha" /> + <param name="l1_ratio" type="float" label="l1_ratio" value="0.15" help="--l1_ratio" /> + <param name="fit_intercept" type="boolean" label="fit_intercept" value="true" help="--fit_intercept" /> + <param name="max_iter" type="integer" label="max_iter" value="1000" help="--max_iter" /> + <param name="tol" type="float" label="tol" value="1e-3" help="--tol" /> + <param name="shuffle" type="boolean" label="shuffle" value='true' help="--shuffle" /> + <param name="verbose" type="integer" label="verbose" value="0" help="--verbose" /> + <param name="epsilon" type="float" label="epsilon" value="0.1" help="--epsilon" /> + <param name="n_jobs" type="text" label="n_jobs" value="none" help="--n_jobs" /> + <param name="random_state" type="text" label="random_state" value="none" help="--random_state" /> + <param name="learning_rate" type="select" label="learning_rate" argument="" help="--learning_rate" > + <option value="constant" selected="true" > constant </option> + <option value="optimal" > optimal </option> + <option value="invscaling"> invscaling </option> + <option value="adaptive"> adaptive </option> + </param> + <param name="eta0" type="float" label="eta0" value="1e-3" help="--eta0" /> + <param name="power_t" type="float" label="power_t" value="0.5" help="--power_t" /> + <param name="early_stopping" type="boolean" label="early_stopping" value="false" help="--early_stopping" /> + <param name="validation_fraction" type="float" label="validation_fraction" value="0.1" help="--validation_fraction" /> + <param name="n_iter_no_change" type="integer" label="n_iter_no_change" value="5" help="--n_iter_no_change" /> + <param name="warm_start" type="boolean" label="warm_start" value='false' help="--warm_start" /> + <param name="average" type="boolean" label="average" value="false" help="--average" /> + </when> + </conditional> + </when> + + <when value="DTC"> + <conditional name="settings"> + <param name="advanced" type="select" label="Specify advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + <when value="simple"> + </when> + + <when value="advanced"> + <param name="criterion" type="select" label="criterion" argument="" help="--criterion" > + <option value="gini" selected="true" > gini </option> + <option value="entropy"> entropy </option> + </param> + <param name="splitter" type="select" label="splitter" argument="" help="--splitter" > + <option value="best" selected="true" > best </option> + <option value="random"> random </option> + </param> + <param name="max_depth" type="integer" label="10" value="10" help="--max_depth" /> + <param name="min_samples_split" type="float" label="min_samples_split" value="2" help="--min_samples_split" /> + <param name="min_samples_leaf" type="float" label="min_weight_fraction_leaf" value="1" help="--min_weight_fraction_leaf" /> + <param name="min_weight_fraction_leaf" type="float" label="min_weight_fraction_leaf" value="0.0" help="--min_weight_fraction_leaf" /> + <param name="max_features" type="text" label="max_features" value='none' help="--max_features" > + </param> + <param name="random_state" type="integer" label="random_state" value="10" help="--random_state" /> + <param name="max_leaf_nodes" type="integer" label="max_leaf_nodes" value="0" help="--max_leaf_nodes" /> + <param name="min_impurity_decrease" type="float" label="min_impurity_decrease" value="0.0" help="--min_impurity_decrease" /> + <param name="min_impurity_split" type="float" label="min_impurity_split" value="1e-7" help="--min_impurity_split" /> + <param name="presort" type="text" label="presort" value="deprecated" help="--presort" /> + <param name="ccpalpha" type="float" label="ccpalpha" value="0.0" help="--ccpalpha" /> + </when> + </conditional> + </when> + + <when value="GBC"> + <conditional name="settings"> + <param name="advanced" type="select" label="Specify advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + <when value="simple"> + </when> + + <when value="advanced"> + <param name="loss" type="select" label="loss" argument="" help="loss" > + <option value="simple" selected="true" > simple </option> + <option value="advanced">advanced</option> + </param> + <param name="learning_rate" type="float" label="learning_rate" value="0.1" help="--learning_rate" /> + <param name="n_estimators" type="integer" label="n_estimators" value="100" help="--n_estimators" /> + <param name="subsample" type="float" label="subsample" value="1.0" help="--subsample" /> + <param name="criterion" type="select" label="criterion" argument="" help="--criterion" > + <option value="mse" selected="true">mse</option> + <option value="friedman_mse">friedman_mse</option> + <option value="mae" > mae </option> + </param> + <param name="min_samples_split" type="text" label="min_samples_split" value="2" help="--min_samples_split" /> + <param name="min_samples_leaf" type="text" label="min_samples_leaf" value="1" help="--min_samples_leaf" /> + <param name="min_weight_fraction_leaf" type="float" label="min_weight_fraction_leaf" value="0.0" help="--min_weight_fraction_leaf" /> + <param name="max_depth" type="integer" label="max_depth" value="3" help="--max_depth" /> + <param name="min_impurity_decrease" type="float" label="min_impurity_decrease" value="0.0" help="--min_impurity_decrease" /> + <param name="min_impurity_split" type="float" label="min_impurity_split" value="1e-7" help="--min_impurity_split" /> + <param name="init" type="select" label="init" argument="" help="init" > + <option value="none" selected="true">None</option> + <option value="Zero">Zero</option> + </param> + <param name="random_state" type="text" label="random_state" value="none" help="--random_state"/> + <param name="max_features" type="text" label="max_features" value="none" help="--max_features" /> + <param name="verbose" type="integer" label="verbose" value="0" help="--verbose" /> + <param name="max_leaf_nodes" type="text" label="max_leaf_nodes" value="none" help="--max_leaf_nodes" /> + <param name="warm_start" type="boolean" label="warm_start" value='false' help="--warm_start" /> + <param name="presort" type="text" label="presort" value="deprecated" help="--presort" /> + <param name="validation_fraction" type="float" label="validation_fraction" value="0.1" help="--validation_fraction" /> + <param name="n_iter_no_change" type="text" label="n_iter_no_change" value="none" help="--n_iter_no_change" /> + <param name="tol" type="float" label="tol" value="1e-4" help="--tol" /> + <param name="ccpalpha" type="float" label="ccpalpha" value="0.0" help="--ccpalpha" /> + </when> + </conditional> + </when> + + <when value="RFC"> + <conditional name="settings"> + <param name="advanced" type="select" label="Specify advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + <when value="simple"> + </when> + <when value="advanced"> + <param name="n_estimators" type="integer" label="n_estimators" value="100" help="--n_estimators" /> + <param name="criterion" type="select" label="criterion" argument="" help="--criterion" > + <option value="gini" selected="true"> gini </option> + <option value="entropy">entropy</option> + </param> + <param name="max_depth" type="text" label="max_depth" value="none" help="--max_depth" /> + <param name="min_samples_split" type="text" label="min_samples_split" value="2" help="--min_impurity_split" /> + <param name="min_samples_leaf" type="text" label="min_samples_leaf" value="1" help="--min_samples_leaf" /> + <param name="min_weight_fraction_leaf" type="float" label="min_weight_fraction_leaf" value="0" help="--min_weight_fraction_leaf" /> + <param name="max_features" type="text" label="max_features" value='auto' help="--max_features" > + + </param> + <param name="max_leaf_nodes" type="text" label="max_leaf_nodes" value="none" help="--max_leaf_nodes" /> + <param name="min_impurity_decrease" type="float" label="min_impurity_decrease" value="0" help="--min_impurity_decrease" /> + <param name="min_impurity_split" type="float" label="min_impurity_split" value="1e-7" help="--min_impurity_split" /> + <param name="bootstrap" type="boolean" label="bootstrap" value="true" help="--bootstrap" /> + <param name="oob_score" type="boolean" label="oob_score" value="false" help="--oob_score" /> + <param name="n_jobs" type="text" label="n_jobs" value="none" help="--n_jobs" /> + <param name="random_state" type="text" label="random_state" value="none" help="--random_state" /> + <param name="verbose" type="integer" label="verbose" value="0" help="--verbose" /> + <param name="warm_start" type="boolean" label="warm_start" help="--warm_start" /> + <param name="ccp_alpha" type="float" label="ccp_alpha" value="0.0" help="--ccp_alpha" /> + <param name="max_samples" type="text" label="max_samples" value="none" help="--max_samples" /> + </when> + </conditional> + </when> + + <when value="LRC"> + <conditional name="settings"> + <param name="advanced" type="select" label="Specify advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + <when value="simple"> + </when> + <when value="advanced"> + <param name="penalty" type="select" label="fit_intercept" argument="" help="--fit_intercept" > + <option value="l2" selected="true"> l1 </option> + <option value="l1" > l2 </option> + <option value="elastic" > elastic </option> + <option value="None" > None </option> + </param> + <param name="dual" type="boolean" label="dual" value="false" help="--dual" /> + <param name="tol" type="float" label="tol" value="1e-4" help="--tol" /> + <param name="C" type="float" label="C" value="1.0" help="--C" /> + <param name="fit_intercept" type="boolean" label="fit_intercept" value="true" help="--fit_intercept" /> + <param name="intercept_scaling" type="float" label="intercept_scaling" value="1.0" help="intercept_scaling" /> + <param name="random_state" type="text" label="random_state" value="none" help="--random_state" /> + <param name="solver" type="select" label="solver" argument="" help="--solver" > + <option value="newton-cg" > newton-cg </option> + <option value="lbfgs" selected="true" > lbfgs </option> + <option value="saga" > saga </option> + <option value="sag" > sag </option> + <option value="liblinear" >liblinear </option> + </param> + <param name="max_iter" type="integer" label="max_iter" value="100" help="--max_iter" /> + <param name="multi_class" type="select" label="multi_class" argument="" help="--multi_class" > + <option value="auto" selected="true" > auto </option> + <option value="ovr" > ovr </option> + <option value="multinomial" > multinomial </option> + </param> + <param name="verbose" type="integer" label="verbose" value="0" help="--verbose" /> + <param name="warm_start" type="boolean" label="warm_start" value="false" help="--warm_start" /> + <param name="n_jobs" type="text" label="n_jobs" value="none" help="--n_jobs" /> + <param name="l1_ratio" type="text" label="l1_ratio" value="none" help="--l1_ratio" /> + </when> + </conditional> + </when> + + <when value="KNC"> + <conditional name="settings"> + <param name="advanced" type="select" label="Specify advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + + <when value="simple"> + </when> + + <when value="advanced"> + <param name="n_neighbors" type="integer" value="5" label="Number of neighbors to use" argument="--n_neighbors" help="Number of neighbors to use" /> + <param name="weights" type="select" label="Weight function" argument="--weights" help="weight function used in prediction. Possible values:" > + <option value="uniform" selected="true" > Uniform </option> + <option value="distance" > Distance </option> + </param> + <param name="p" type="integer" label="Power parameter" value="2" help="Power parameter for the Minkowski metric." /> + <param name="leaf_size" type="integer" label="Leaf size" value="30" argument="--leaf_size" help="Leaf size passed to BallTree or KDTree." /> + <param name="algorithm" type="select" label="solver" argument="" help="--solver" > + <option value="ball_tree" > BallTree </option> + <option value="kd_tree" > KDTree </option> + <option value="brute"> Brute-Force </option> + <option value="auto" selected="true"> Auto</option> + </param> + <param name="metric" type="select" label="Distance metric" help="The distance metric to use for the tree." > + <option value="minkowski" selected="true"> Minkowski </option> + <option value="precomputed" >Precomputed </option> + </param> + <param name="n_jobs" type="integer" label="N-jobs" value="-1" help="The number of parallel jobs to run for neighbors search" /> + </when> + </conditional> + + </when> + + <when value="GNBC"> + <conditional name="settings"> + <param name="advanced" type="select" label="Specify advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + <when value="simple"> + </when> + <when value="advanced"> + <param name="var_smoothing" type="float" label="var_smoothing" value="1e-9" help="--var_smoothing" /> + </when> + </conditional> + </when> + + <when value="MLP"> + <conditional name="settings"> + <param name="advanced" type="select" label="Specify advanced parameters"> + <option value="simple" selected="true">No, use program defaults.</option> + <option value="advanced">Yes, see full parameter list.</option> + </param> + <when value="simple"> + </when> + <when value="advanced"> + <param name="hidden_layer_sizes" type="text" label="hidden_layer_sizes" value="100," help="--hidden_layer_sizes" /> + <param name="activation" type='select' label="activation" help="--hidden_layer_sizes" > + <option value="indentity" > indentity </option> + <option value="logistic" > logistic </option> + <option value="tanh" > tanh </option> + <option value="relu" selected="true" > relu </option> + </param> + + <param name="solver" type="select" label="solver" help="--solver" > + <option value="lbfgs" > lbfgs </option> + <option value="sgd" > sgd </option> + <option value="adam" selected="true" >adam </option> + </param> + + <param name="alpha" type="float" value="0.0001" label="alpha" help="--alpha" /> + <param name="batch_size" type="text" value="auto" label="batch_size" help="--batch_size" /> + <param name="learning_rate" type="select" label="learning_rate" help="--learning_rate" > + <option value="constant" selected="true" >constant </option> + <option value="invscaling" >invscaling </option> + <option value="adaptive" >adaptive </option> + </param> + <param name="learning_rate_int" type="float" value="0.001" label="learning_rate_int" help="--learning_rate_int" /> + <param name="power_t" type="float" value="0.5" label="power_t" help="--power_t" /> + <param name="max_iter" type="integer" value="200" label="max_iter" help="--max_iter" /> + <param name="shuffle" type="boolean" label="shuffle" value="true" help="--shuffle" /> + <param name="random_state" type="text" label="random_state" value="none" help="--random_state" /> + <param name="tol" type="float" label="tol" value="1e-4" help="--tol" /> + <param name="verbose" type="boolean" label="verbose" value="false" help="--verbose" /> + <param name="warm_start" type="boolean" label="warm_start" value="false" help="--warm_start" /> + <param name="momentum" type="float" label="momentum" value="0.9" help="--momentum" /> + <param name="nesterovs_momentum" type="boolean" label="nesterovs_momentum" value="true" help="--nesterovs_momentum" /> + <param name="early_stopping" type="boolean" label="early_stopping" value="false" help="--early_stopping" /> + <param name="validation_fraction" type="float" label="validation_fraction" value="0.1" help="--validation_fraction" /> + <param name="beta_1" type="float" label="beta_1" value="0.9" help="--beta_1" /> + <param name="beta_2" type="float" label="beta_1" value="0.999" help="--beta_2" /> + <param name="epsilon" type="float" label="epsilon" value="1e-8" help="--epsilon" /> + <param name="n_iter_no_change" type="integer" label="n_iter_no_change" value="10" help="--n_iter_no_change" /> + <param name="max_fun" type="integer" label="max_fun" value="15000" help="--max_fun" /> + </when> + </conditional> + </when> + + </conditional> + + <conditional name='TestMethods'> + <param name="SelTestMethods" type="select" label="Choose the Test method" argument="--TestMethod" help="Data testing method"> + <option value="Internal">Internal</option> + <option value="TestSplit">TestSplit</option> + <option value="External">External</option> + <option value="Predict">Predict</option> + </param> + <when value="Internal"> + <param name="nFolds" type="integer" label="Cross validation" value="5" min="5" max="10" argument="--nfold" help="Cross validation"/> + </when> + <when value="TestSplit"> + <param name="TestSplit" type="float" label="Split Training data" value="0.2" min="0.0" max="1.0" argument="-X" help="Split Training data"/> + </when> + <when value="External"> + <param name="input2" type="data" label="Test data file" format="tabular" argument="--TestFile" help="Tabular file with text data"/> + </when> + <when value="Predict"> + <param name="input2" type="data" format="Unlabeled data file" argument="--TestFile" help="Unlabeled data for predict"/> + </when> + </conditional> + + <param name="scalling" type="select" label="Data scalling options" argument="--SelectScaler" help="Data scalling options"> + <option value="Min_Max"> Min_Max </option> + <option value="Standard_Scaler"> Standard_Scaler </option> + <option value="No_Scaler"> No_Scaler </option> + </param> + </inputs> + + <outputs> + <data name='output1' format='tabular' label="${tool.name} on $on_string - ${SelMLAlgo.MLAlgo} (tabular)" /> + <data name='output2' format='html' label="${tool.name} on $on_string - ${SelMLAlgo.MLAlgo} (webpage)" /> + </outputs> + + + <tests> + + <test> + <param name="input1" value="test.tsv"/> + <param name="MLAlgo" value="SVMC" /> + <param name="scalling" value="Min_Max"/> + <output name="output1" file="test1/report_dir/SVMC.tsv" lines_diff="2"/> + <output name="output2" file="test1/report_dir/SVMC.html" lines_diff="2" /> + </test> + + <test> + <param name="input1" value="test.tsv"/> + <param name="MLAlgo" value="GNBC" /> + <param name="scalling" value="Min_Max"/> + <output name="output1" file="test2/GNBC.tsv" lines_diff='2'/> + <output name="output2" file="test2/report_dir/GNBC.html" lines_diff='2'/> + </test> + + <test> + <param name="input1" value="test.tsv"/> + <param name="MLAlgo" value="SGDC" /> + <param name="scalling" value="Min_Max"/> + <output name="output1" file="test3/SGDC.tsv" lines_diff='2'/> + <output name="output2" file="test3/report_dir/SGDC.html" lines_diff='2'/> + </test> + + <test> + <param name="input1" value="test.tsv"/> + <param name="MLAlgo" value="DTC" /> + <param name="scalling" value="Min_Max"/> + <output name="output1" file="test4/DTC.tsv" lines_diff='2' /> + <output name="output2" file="test4/report_dir/DTC.html" lines_diff='2'/> + </test> + + <test> + <param name="input1" value="test.tsv"/> + <param name="MLAlgo" value="GBC" /> + <param name="scalling" value="Min_Max"/> + <output name="output1" file="test5/GBC.tsv" lines_diff='2' /> + <output name="output2" file="test5/report_dir/GBC.html" lines_diff='2'/> + </test> + + <test> + <param name="input1" value="test.tsv"/> + <param name="MLAlgo" value="RFC" /> + <param name="scalling" value="Min_Max"/> + <output name="output1" file="test6/RFC.tsv" lines_diff='2' /> + <output name="output2" file="test6/report_dir/RFC.html" lines_diff='2'/> + </test> + + <test> + <param name="input1" value="test.tsv"/> + <param name="MLAlgo" value="LRC" /> + <param name="scalling" value="Min_Max"/> + <output name="output1" file="test7/LRC.tsv" lines_diff='2' /> + <output name="output2" file="test7/report_dir/LRC.html" lines_diff='2'/> + </test> + + <test> + <param name="input1" value="test.tsv"/> + <param name="MLAlgo" value="KNC" /> + <param name="scalling" value="Min_Max"/> + <output name="output1" file="test8/KNC.tsv" lines_diff='2'/> + <output name="output2" file="test8/report_dir/KNC.html" lines_diff='2'/> + </test> + + <test> + <param name="input1" value="test.tsv"/> + <param name="MLAlgo" value="MLP" /> + <param name="scalling" value="Min_Max"/> + <output name="output1" file="test9/MLP.tsv" lines_diff='2'/> + <output name="output2" file="test9/report_dir/MLP.html" lines_diff='2'/> + </test> + + </tests> + + + + <help><![CDATA[ +.. class:: infomark + +**What it does** + +This tool builds a machine learning model from the given descriptor set based on the binary class label. There are 8 different machine learning algorithms that have been implemented up to 10 fold cross-validation. We have also implemented standard scaler and MinMaxScaler normalization. + + * **Support Vector Machine Classifier** + * **Stochastic gradient descent Classifier** + * **Decision tree** + * **Gradient boosting Classifier** + * **Random Forest Classifier** + * **Logistic regression Classifier** + * **k-nearest neighbors Classifier** + * **Gaussian naive Bayes Classifier** + * **Multilayer perceptron Classifier** + +A detail Description of all the algorithms can be found at sklearn (https://scikit-learn.org/stable/) + +----- + +**Inputs** + * **Training File** Tabulalr files with labeled peptide descriptor data. + * **Select Machine Learning algorithms** Select algorithm. + * **Select Advanced Parameters** Select the advance parameter details of each of the parameters that can be found on sklearn website. + * **Select the test method** (predict or internal test) + * **Cross Validation** Up to 10 fold cross-validation. + * **Method to Scale the data** MinMaxScaler and standard scaler. + +----- + +**Outputs** + * Tabular file with the various performance scores (accurracy, precision, recall, f1-score, and AUC score). ]]></help> + +<citations> + <citation type="bibtex"> + @misc{PDAUGGITHUB, + author = {Joshi, Jayadev and Blankenberg, Daniel}, + year = {2020}, + title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = + {https://github.com/jaidevjoshi83/pdaug.git}, + +}</citation> + + <citation type="bibtex"> + @article{scikit-learn, + title={Scikit-learn: Machine Learning in {P}ython}, + author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V. + and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P. + and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and + Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.}, + journal={Journal of Machine Learning Research}, + volume={12}, + pages={2825--2830}, + year={2011} + }</citation> +</citations> +</tool> + + +