Mercurial > repos > iuc > filter_tabular
diff macros.xml @ 13:4d5aae46f850 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
| author | iuc |
|---|---|
| date | Thu, 19 Aug 2021 19:39:58 +0000 |
| parents | 37cde8134c6a |
| children | 557ec8d7087d |
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--- a/macros.xml Sat Jun 19 14:16:06 2021 +0000 +++ b/macros.xml Thu Aug 19 19:39:58 2021 +0000 @@ -32,7 +32,12 @@ #elif $fi.filter.filter_type == 'select_columns': #set $filter_dict = dict() #set $filter_dict['filter'] = str($fi.filter.filter_type) - #set $filter_dict['columns'] = [int(str($ci).replace('c','')) for $ci in str($fi.filter.columns).split(',')] + #set $filter_dict['columns'] = [int($c) for $c in str($fi.filter.columns).replace('c','').split(',')] + #silent $input_filters.append($filter_dict) + #elif $fi.filter.filter_type == 'select_column_slices': + #set $filter_dict = dict() + #set $filter_dict['filter'] = str($fi.filter.filter_type) + #set $filter_dict['columns'] = [$c for $c in str($fi.filter.columns).split(',')] #silent $input_filters.append($filter_dict) #elif $fi.filter.filter_type == 'replace': #set $filter_dict = dict() @@ -53,6 +58,11 @@ #set $filter_dict['filter'] = str($fi.filter.filter_type) #set $filter_dict['column_text'] = str($fi.filter.column_text) #silent $input_filters.append($filter_dict) + #elif str($fi.filter.filter_type).endswith('pend_dataset_name'): + #set $filter_dict = dict() + #set $filter_dict['filter'] = str($fi.filter.filter_type).replace('dataset_name', 'text') + #set $filter_dict['column_text'] = $dataset_name + #silent $input_filters.append($filter_dict) #elif $fi.filter.filter_type == 'normalize': #set $filter_dict = dict() #set $filter_dict['filter'] = str($fi.filter.filter_type) @@ -129,9 +139,12 @@ <option value="comment">comment char</option> <option value="regex">by regex expression matching</option> <option value="select_columns">select columns</option> + <option value="select_column_slices">select columns by indices/slices</option> <option value="replace">regex replace value in column</option> <option value="prepend_line_num">prepend a line number column</option> <option value="append_line_num">append a line number column</option> + <option value="prepend_dataset_name">prepend a column with the dataset name</option> + <option value="append_dataset_name">append a column with the dataset name</option> <option value="prepend_text">prepend a column with the given text</option> <option value="append_text">append a column with the given text</option> <option value="normalize">normalize list columns, replicates row for each item in list</option> @@ -147,6 +160,8 @@ </when> <when value="prepend_line_num"/> <when value="append_line_num"/> + <when value="prepend_dataset_name"/> + <when value="append_dataset_name"/> <when value="prepend_text"> <param name="column_text" type="text" value="" label="text for column"> </param> @@ -172,6 +187,26 @@ <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator> </param> </when> + <when value="select_column_slices"> + <param name="columns" type="text" value="" label="enter indices or slices of the columns to keep"> + <help><![CDATA[ Python offset indexes or slices. Examples: + <ul> + <li>Column offset indexes: 0,3,1 (selects the first,fourth, and second columns)</li> + <li>Negative column numbers: -1,-2 (selects the last, and second last columns)</li> + <li>python slices ( slice(start, stop[, step]) select a range of columns): <li> + <ul> + <li>0:3 or :3 (selects the first 3 columns)</li> + <li>3:5 (selects the fourth and fifth columns)</li> + <li>2: (selects all columns after the second)</li> + <li>-2: (selects the last 2 columns)</li> + <li>2::-1 (selects the first 3 columns n reverse order: third,second,first)</li> + </ul> + </ul> + ]]></help> + <validator type="regex" message="Column ordinal positions separated by commas">^(-?[1-9]\d*|((-?\d+)?:(-?\d*(:-?\d*)?)))(,(-?[1-9]\d*|((-?\d+)?:(-?\d*(:-?\d*)?))))*$</validator> + </param> + </when> + <when value="replace"> <param name="column" type="text" value="" label="enter column number to replace" help="example: 1 or c1 (selects the first column)"> @@ -211,21 +246,24 @@ <![CDATA[ **Input Line Filters** - As a tabular file is being read, line filters may be applied. - - :: + As a tabular file is being read, line filters may be applied: - - skip leading lines skip the first *number* of lines - - comment char omit any lines that start with the specified comment character - - by regex expression matching *include/exclude* lines the match the regex expression - - select columns choose to include only selected columns in the order specified - - regex replace value in column replace a field in a column using a regex substitution (good for date reformatting) - - regex replace value in column add a new column using a regex substitution of a column value - - prepend a line number column each line has the ordinal value of the line read by this filter as the first column - - append a line number column each line has the ordinal value of the line read by this filter as the last column - - prepend a text column each line has the text string as the first column - - append a text column each line has the text string as the last column - - normalize list columns replicates the line for each item in the specified list *columns* + - skip leading lines - skip the first *number* of lines + - comment char - omit any lines that start with the specified comment character + - by regex expression matching - *include/exclude* lines that match the regex expression + - select columns - choose to include only selected columns in the order specified + - select columns by indices/slices - *indices or slices* of the columns to keep (python_list_ indexing) + - regex replace value in column - replace a field in a column using a regex substitution (good for date reformatting) + - regex replace value in column - add a new column using a regex substitution of a column value + - prepend a line number column - each line has the *ordinal* value of the line read by this filter as the first column + - append a line number column - each line has the *ordinal* value of the line read by this filter as the last column + - prepend a text column - each line has the text string as the first column + - append a text column - each line has the text string as the last column + - prepend the dataset name - each line has the *dataset name* as the first column + - append the dataset name - each line has the *dataset name* as the last column + - normalize list columns - replicates the line for each item in the specified list *columns* + +.. _python_list: https://docs.python.org/3/library/stdtypes.html#common-sequence-operations ]]> </token> @@ -284,13 +322,13 @@ 0 Jane Doe 1978-05-24 5 3 1 James Smith 1980-10-20 Spot 6 4 - Filter 6 - append a line number column: + Filter 6 - select columns by indices/slices: '1:6' - 2 Paula Brown 1978-05-24 Rex dog 3 1 1 - 2 Paula Brown 1978-05-24 Fluff cat 3 1 2 - 1 Steven Jones 1974-04-04 Allie cat 4 2 3 - 0 Jane Doe 1978-05-24 5 3 4 - 1 James Smith 1980-10-20 Spot 6 4 5 + Paula Brown 1978-05-24 Rex dog + Paula Brown 1978-05-24 Fluff cat + Steven Jones 1974-04-04 Allie cat + Jane Doe 1978-05-24 + James Smith 1980-10-20 Spot ]]> </token>