| Previous changeset 27:a9474cdda506 (2019-09-13) Next changeset 29:f12dc92b6699 (2019-11-01) |
|
Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty" |
|
modified:
generalized_linear.xml main_macros.xml ml_visualization_ex.py stacking_ensembles.py |
| b |
| diff -r a9474cdda506 -r 63417d0acc72 generalized_linear.xml --- a/generalized_linear.xml Fri Sep 13 12:17:00 2019 -0400 +++ b/generalized_linear.xml Wed Oct 02 03:43:23 2019 -0400 |
| [ |
| @@ -45,7 +45,8 @@ #else: with open("$selected_tasks.infile_model", 'rb') as model_handler: classifier_object = load_model(model_handler) -data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=None, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False ) +header = 'infer' if params["selected_tasks"]["header"] else None +data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False) prediction = classifier_object.predict(data) prediction_df = pandas.DataFrame(prediction, columns=["predicted"]) res = pandas.concat([data, prediction_df], axis=1) |
| b |
| diff -r a9474cdda506 -r 63417d0acc72 main_macros.xml --- a/main_macros.xml Fri Sep 13 12:17:00 2019 -0400 +++ b/main_macros.xml Wed Oct 02 03:43:23 2019 -0400 |
| b |
| @@ -421,27 +421,46 @@ <xml name="sl_mixed_input"> <conditional name="input_options"> - <param name="selected_input" type="select" label="Select input type:"> - <option value="tabular" selected="true">tabular data</option> - <option value="sparse">sparse matrix</option> - <option value="seq_fasta">sequnences in a fasta file</option> - <option value="refseq_and_interval">reference genome and intervals</option> - </param> - <when value="tabular"> - <expand macro="samples_tabular" multiple1="true" multiple2="false"/> - </when> - <when value="sparse"> - <expand macro="sparse_target"/> - </when> - <when value="seq_fasta"> - <expand macro="inputs_seq_fasta"/> - </when> - <when value="refseq_and_interval"> - <expand macro="inputs_refseq_and_interval"/> - </when> + <expand macro="data_input_options"/> + <expand macro="data_input_whens"/> </conditional> </xml> + <xml name="sl_mixed_input_plus_sequence"> + <conditional name="input_options"> + <expand macro="data_input_options"> + <option value="seq_fasta">sequnences in a fasta file</option> + <option value="refseq_and_interval">reference genome and intervals</option> + </expand> + <expand macro="data_input_whens"> + <when value="seq_fasta"> + <expand macro="inputs_seq_fasta"/> + </when> + <when value="refseq_and_interval"> + <expand macro="inputs_refseq_and_interval"/> + </when> + </expand> + </conditional> + </xml> + + <xml name="data_input_options"> + <param name="selected_input" type="select" label="Select input type:"> + <option value="tabular" selected="true">tabular data</option> + <option value="sparse">sparse matrix</option> + <yield/> + </param> + </xml> + + <xml name="data_input_whens"> + <when value="tabular"> + <expand macro="samples_tabular" multiple1="true" multiple2="false"/> + </when> + <when value="sparse"> + <expand macro="sparse_target"/> + </when> + <yield/> + </xml> + <xml name="input_tabular_target"> <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:"/> <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" /> |
| b |
| diff -r a9474cdda506 -r 63417d0acc72 ml_visualization_ex.py --- a/ml_visualization_ex.py Fri Sep 13 12:17:00 2019 -0400 +++ b/ml_visualization_ex.py Wed Oct 02 03:43:23 2019 -0400 |
| [ |
| @@ -146,7 +146,8 @@ precision["micro"], recall["micro"], _ = precision_recall_curve( df1.values.ravel(), df2.values.ravel(), pos_label=pos_label) ap['micro'] = average_precision_score( - df1.values, df2.values, average='micro', pos_label=pos_label or 1) + df1.values, df2.values, average='micro', + pos_label=pos_label or 1) data = [] for key in precision.keys(): @@ -201,7 +202,7 @@ ) data.append(trace) - trace = go.Scatter(x=[0, 1], y=[0, 1], + trace = go.Scatter(x=[0, 1], y=[0, 1], mode='lines', line=dict(color='black', dash='dash'), showlegend=False) |
| b |
| diff -r a9474cdda506 -r 63417d0acc72 stacking_ensembles.py --- a/stacking_ensembles.py Fri Sep 13 12:17:00 2019 -0400 +++ b/stacking_ensembles.py Wed Oct 02 03:43:23 2019 -0400 |
| b |
| @@ -11,7 +11,7 @@ from sklearn import ensemble from galaxy_ml.utils import (load_model, get_cv, get_estimator, - get_search_params) + get_search_params) warnings.filterwarnings('ignore') |