Mercurial > repos > bgruening > scipy_sparse
comparison main_macros.xml @ 10:5c8b6eff7975 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
| author | bgruening |
|---|---|
| date | Tue, 05 Jun 2018 06:48:16 -0400 |
| parents | 4aadc6731c01 |
| children | 102c8bae2e9c |
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| 9:4aadc6731c01 | 10:5c8b6eff7975 |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <token name="@VERSION@">0.9</token> | 2 <token name="@VERSION@">0.9</token> |
| 3 | 3 |
| 4 <token name="@COLUMNS_FUNCTION@"> | 4 <token name="@COLUMNS_FUNCTION@"> |
| 5 def read_columns(f, c, return_df=False, **args): | 5 def read_columns(f, c=None, c_option='by_index_number', return_df=False, **args): |
| 6 data = pandas.read_csv(f, **args) | 6 data = pandas.read_csv(f, **args) |
| 7 cols = c.split (',') | 7 if c_option == 'by_index_number': |
| 8 cols = map(int, cols) | 8 cols = list(map(lambda x: x - 1, c)) |
| 9 cols = list(map(lambda x: x - 1, cols)) | 9 data = data.iloc[:,cols] |
| 10 data = data.iloc[:,cols] | |
| 11 y = data.values | 10 y = data.values |
| 12 if return_df: | 11 if return_df: |
| 13 return y, data | 12 return y, data |
| 14 else: | 13 else: |
| 15 return y | 14 return y |
| 16 return y | 15 return y |
| 17 </token> | 16 </token> |
| 18 | 17 |
| 19 ## generate an instance for one of sklearn.feature_selection classes | 18 ## generate an instance for one of sklearn.feature_selection classes |
| 20 ## must call "@COLUMNS_FUNCTION@" | |
| 21 <token name="@FEATURE_SELECTOR_FUNCTION@"> | 19 <token name="@FEATURE_SELECTOR_FUNCTION@"> |
| 22 def feature_selector(inputs): | 20 def feature_selector(inputs): |
| 23 selector = inputs["selected_algorithm"] | 21 selector = inputs["selected_algorithm"] |
| 24 selector = getattr(sklearn.feature_selection, selector) | 22 selector = getattr(sklearn.feature_selection, selector) |
| 25 options = inputs["options"] | 23 options = inputs["options"] |
| 426 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/> | 424 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/> |
| 427 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/> | 425 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/> |
| 428 <yield/> | 426 <yield/> |
| 429 </xml> | 427 </xml> |
| 430 | 428 |
| 431 <xml name="samples_tabular" token_multiple1="False" token_multiple2="False"> | 429 <xml name="samples_tabular" token_multiple1="false" token_multiple2="false"> |
| 432 <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/> | 430 <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/> |
| 433 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | 431 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> |
| 434 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/> | 432 <conditional name="column_selector_options_1"> |
| 433 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/> | |
| 434 </conditional> | |
| 435 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels:"/> | 435 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels:"/> |
| 436 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | 436 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> |
| 437 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/> | 437 <conditional name="column_selector_options_2"> |
| 438 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE2@" infile="infile2"/> | |
| 439 </conditional> | |
| 438 <yield/> | 440 <yield/> |
| 441 </xml> | |
| 442 | |
| 443 <xml name="samples_column_selector_options" token_column_option="selected_column_selector_option" token_col_name="col1" token_multiple="False" token_infile="infile1"> | |
| 444 <param name="@COLUMN_OPTION@" type="select" label="Choose how to select data by column:"> | |
| 445 <option value="by_index_number" selected="true">Select columns by column index number(s)</option> | |
| 446 <!-- | |
| 447 <option value="by_header_name">Select columns by column header name(s)</option> | |
| 448 <option value="all_but_by_index_number">All columns but by column index number(s)</option> | |
| 449 <option value="all_but_by_header_name">All columns but by column header name(s)</option> | |
| 450 --> | |
| 451 <option value="all_columns">All columns</option> | |
| 452 </param> | |
| 453 <when value="by_index_number"> | |
| 454 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" data_ref="@INFILE@" label="Select target column(s):"/> | |
| 455 </when> | |
| 456 <when value="all_columns"> | |
| 457 </when> | |
| 439 </xml> | 458 </xml> |
| 440 | 459 |
| 441 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False"> | 460 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False"> |
| 442 <conditional name="true_columns"> | 461 <conditional name="true_columns"> |
| 443 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:"> | 462 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:"> |
| 468 </xml> | 487 </xml> |
| 469 | 488 |
| 470 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False"> | 489 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False"> |
| 471 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/> | 490 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/> |
| 472 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | 491 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> |
| 473 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select the target column:"/> | 492 <conditional name="column_selector_options_1"> |
| 493 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/> | |
| 494 </conditional> | |
| 474 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/> | 495 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/> |
| 475 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | 496 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> |
| 476 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/> | 497 <conditional name="column_selector_options_2"> |
| 498 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE@" infile="infile2"/> | |
| 499 </conditional> | |
| 477 </xml> | 500 </xml> |
| 478 | 501 |
| 479 <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."> | 502 <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."> |
| 480 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):"> | 503 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):"> |
| 481 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/> | 504 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/> |