| Previous changeset 2:dd502cb0d567 (2018-05-30) Next changeset 4:60b8a683ba99 (2018-06-06) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888 |
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modified:
main_macros.xml model_validation.xml |
| b |
| diff -r dd502cb0d567 -r 424d8d21744d main_macros.xml --- a/main_macros.xml Wed May 30 08:27:01 2018 -0400 +++ b/main_macros.xml Tue Jun 05 06:48:01 2018 -0400 |
| [ |
| @@ -2,12 +2,11 @@ <token name="@VERSION@">0.9</token> <token name="@COLUMNS_FUNCTION@"> -def read_columns(f, c, return_df=False, **args): +def read_columns(f, c=None, c_option='by_index_number', return_df=False, **args): data = pandas.read_csv(f, **args) - cols = c.split (',') - cols = map(int, cols) - cols = list(map(lambda x: x - 1, cols)) - data = data.iloc[:,cols] + if c_option == 'by_index_number': + cols = list(map(lambda x: x - 1, c)) + data = data.iloc[:,cols] y = data.values if return_df: return y, data @@ -17,7 +16,6 @@ </token> ## generate an instance for one of sklearn.feature_selection classes -## must call "@COLUMNS_FUNCTION@" <token name="@FEATURE_SELECTOR_FUNCTION@"> def feature_selector(inputs): selector = inputs["selected_algorithm"] @@ -428,16 +426,37 @@ <yield/> </xml> - <xml name="samples_tabular" token_multiple1="False" token_multiple2="False"> + <xml name="samples_tabular" token_multiple1="false" token_multiple2="false"> <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/> - <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> - <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/> + <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> + <conditional name="column_selector_options_1"> + <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/> + </conditional> <param name="infile2" type="data" format="tabular" label="Dataset containing class labels:"/> - <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> - <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/> + <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> + <conditional name="column_selector_options_2"> + <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE2@" infile="infile2"/> + </conditional> <yield/> </xml> + <xml name="samples_column_selector_options" token_column_option="selected_column_selector_option" token_col_name="col1" token_multiple="False" token_infile="infile1"> + <param name="@COLUMN_OPTION@" type="select" label="Choose how to select data by column:"> + <option value="by_index_number" selected="true">Select columns by column index number(s)</option> + <!-- + <option value="by_header_name">Select columns by column header name(s)</option> + <option value="all_but_by_index_number">All columns but by column index number(s)</option> + <option value="all_but_by_header_name">All columns but by column header name(s)</option> + --> + <option value="all_columns">All columns</option> + </param> + <when value="by_index_number"> + <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" data_ref="@INFILE@" label="Select target column(s):"/> + </when> + <when value="all_columns"> + </when> + </xml> + <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False"> <conditional name="true_columns"> <param name="selected_input1" type="select" label="Select the input type of true labels dataset:"> @@ -470,10 +489,14 @@ <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False"> <param name="infile1" type="data" format="tabular" label="@LABEL1@"/> <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> - <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select the target column:"/> + <conditional name="column_selector_options_1"> + <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/> + </conditional> <param name="infile2" type="data" format="tabular" label="@LABEL2@"/> <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> - <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/> + <conditional name="column_selector_options_2"> + <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE@" infile="infile2"/> + </conditional> </xml> <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format."> |
| b |
| diff -r dd502cb0d567 -r 424d8d21744d model_validation.xml --- a/model_validation.xml Wed May 30 08:27:01 2018 -0400 +++ b/model_validation.xml Tue Jun 05 06:48:01 2018 -0400 |
| [ |
| @@ -35,9 +35,15 @@ input_type = params["input_options"]["selected_input"] if input_type=="tabular": header = 'infer' if params["input_options"]["header1"] else None + column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"] + if column_option == "by_index_number": + c = params["input_options"]["column_selector_options_1"]["col1"] + else: + c = None X = read_columns( "$input_options.infile1", - "$input_options.col1", + c = c, + c_option = column_option, sep='\t', header=header, parse_dates=True @@ -46,9 +52,15 @@ X = mmread(open("$input_options.infile1", 'r')) header = 'infer' if params["input_options"]["header2"] else None +column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"] +if column_option == "by_index_number": + c = params["input_options"]["column_selector_options_2"]["col2"] +else: + c = None y = read_columns( "$input_options.infile2", - "$input_options.col2", + c = c, + c_option = column_option, sep='\t', header=header, parse_dates=True @@ -318,7 +330,7 @@ <param name="has_estimator" value="yes"/> <param name="infile1" value="regression_X.tabular" ftype="tabular"/> <param name="header1" value="true" /> - <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> + <param name="selected_column_selector_option" value="all_columns"/> <param name="infile2" value="regression_y.tabular" ftype="tabular"/> <param name="header2" value="true" /> <param name="col2" value="1"/> @@ -336,10 +348,10 @@ <param name="return_type" value="best_score_"/> <param name="infile1" value="regression_X.tabular" ftype="tabular"/> <param name="header1" value="true" /> - <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> + <param name="selected_column_selector_option" value="all_columns"/> <param name="infile2" value="regression_y.tabular" ftype="tabular"/> <param name="header2" value="true" /> - <param name="col2" value="1"/> + <param name="selected_column_selector_option2" value="all_columns"/> <output name="outfile" file="mv_result07.tabular"/> </test> </tests> |