Mercurial > repos > iuc > sqlite_to_tabular
diff macros.xml @ 0:859064f07be4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
| author | iuc |
|---|---|
| date | Tue, 18 Jul 2017 09:07:26 -0400 |
| parents | |
| children | c1b700bc0150 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jul 18 09:07:26 2017 -0400 @@ -0,0 +1,383 @@ +<macros> + <token name="@LINEFILTERS@"> +<![CDATA[ + ## set linefilters to the + #set $input_filters = [] + #for $fi in $linefilters: + #if $fi.filter.filter_type == 'skip': + #set $skip_lines = None + #if str($fi.filter.skip_lines) != '': + #set $skip_lines = int($fi.filter.skip_lines) + #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0: + #set $skip_lines = int($tbl.table.metadata.comment_lines) + #end if + #if $skip_lines is not None: + #set $filter_dict = dict() + #set $filter_dict['filter'] = str($fi.filter.filter_type) + #set $filter_dict['count'] = $skip_lines + #silent $input_filters.append($filter_dict) + #end if + #elif $fi.filter.filter_type == 'comment': + #set $filter_dict = dict() + #set $filter_dict['filter'] = 'regex' + #set $filter_dict['pattern'] = '^(%s).*$' % '|'.join([chr(int(x)).replace('|','[|]') for x in (str($fi.filter.comment_char)).split(',')]) + #set $filter_dict['action'] = 'exclude_match' + #silent $input_filters.append($filter_dict) + #elif $fi.filter.filter_type == 'regex': + #set $filter_dict = dict() + #set $filter_dict['filter'] = str($fi.filter.filter_type) + #set $filter_dict['pattern'] = str($fi.filter.regex_pattern) + #set $filter_dict['action'] = str($fi.filter.regex_action) + #silent $input_filters.append($filter_dict) + #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(',')] + #silent $input_filters.append($filter_dict) + #elif $fi.filter.filter_type == 'replace': + #set $filter_dict = dict() + #set $filter_dict['filter'] = str($fi.filter.filter_type) + #set $filter_dict['column'] = int(str($fi.filter.column).replace('c','')) + #set $filter_dict['pattern'] = str($fi.filter.regex_pattern) + #set $filter_dict['replace'] = str($fi.filter.regex_replace) + #silent $input_filters.append($filter_dict) + #elif str($fi.filter.filter_type).endswith('pend_line_num'): + #set $filter_dict = dict() + #set $filter_dict['filter'] = str($fi.filter.filter_type) + #silent $input_filters.append($filter_dict) + #elif str($fi.filter.filter_type).endswith('pend_text'): + #set $filter_dict = dict() + #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 $fi.filter.filter_type == 'normalize': + #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 $filter_dict['separator'] = str($fi.filter.separator) + #silent $input_filters.append($filter_dict) + #end if + #end for +]]> + </token> + <xml name="macro_line_filters"> + <repeat name="linefilters" title="Filter Tabular Input Lines"> + <conditional name="filter"> + <param name="filter_type" type="select" label="Filter By"> + <option value="skip">skip leading lines</option> + <option value="comment">comment char</option> + <option value="regex">by regex expression matching</option> + <option value="select_columns">select columns</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_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> + </param> + <when value="skip"> + <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" + help="Leave blank to use the comment lines metadata for this dataset" /> + </when> + <when value="comment"> + <param name="comment_char" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are skipped"> + <option value="62">></option> + <option value="64">@</option> + <option value="43">+</option> + <option value="60"><</option> + <option value="42">*</option> + <option value="45">-</option> + <option value="61">=</option> + <option value="124">|</option> + <option value="63">?</option> + <option value="36">$</option> + <option value="46">.</option> + <option value="58">:</option> + <option value="38">&</option> + <option value="37">%</option> + <option value="94">^</option> + <option value="35">#</option> + <option value="33">!</option> + </param> + </when> + <when value="prepend_line_num"/> + <when value="append_line_num"/> + <when value="prepend_text"> + <param name="column_text" type="text" value="" label="text for column"> + </param> + </when> + <when value="append_text"> + <param name="column_text" type="text" value="" label="text for column"> + </param> + </when> + <when value="regex"> + <param name="regex_pattern" type="text" value="" label="regex pattern"> + <sanitizer sanitize="False"/> + </param> + <param name="regex_action" type="select" label="action for regex match"> + <option value="exclude_match">exclude line on pattern match</option> + <option value="include_match">include line on pattern match</option> + <option value="exclude_find">exclude line if pattern found</option> + <option value="include_find">include line if pattern found</option> + </param> + </when> + <when value="select_columns"> + <param name="columns" type="text" value="" label="enter column numbers to keep" + help="example: 1,4,2 or c1,c4,c2(selects the first,fourth, and second columns)"> + <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</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)"> + <validator type="regex" message="Column ordinal position separated by commas">^(c?[1-9]\d*)$</validator> + </param> + <param name="regex_pattern" type="text" value="" label="regex pattern"> + <sanitizer sanitize="False"/> + </param> + <param name="regex_replace" type="text" value="" label="replacement expression"> + <sanitizer sanitize="False"/> + </param> + </when> + <when value="normalize"> + <param name="columns" type="text" value="" label="enter column numbers to normalize"> + <help><![CDATA[ + example: 2,4 or c2,c4 (selects the second, and fourth columns) + If multiple columns are selected, they should have the same length and separator on each line + ]]></help> + <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator> + </param> + <param name="separator" type="text" value="," label="List item delimiter in column"> + <sanitizer sanitize="False"/> + <validator type="regex" message="Anything but TAB or Newline">^[^\t\n\r\f\v]+$</validator> + </param> + </when> + </conditional> + </repeat> + </xml> + + <token name="@LINEFILTERS_HELP@"> +<![CDATA[ +**Input Line Filters** + + 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) + - 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* +]]> + </token> + + <token name="@LINEFILTERS_HELP_EXAMPLE@"> +<![CDATA[ +**Line Filtering Example** + *(Six filters are applied as the following file is read)* + + :: + + Input Tabular File: + + #People with pets + Pets FirstName LastName DOB PetNames PetType + 2 Paula Brown 24/05/78 Rex,Fluff dog,cat + 1 Steven Jones 04/04/74 Allie cat + 0 Jane Doe 24/05/78 + 1 James Smith 20/10/80 Spot + + + Filter 1 - append a line number column: + + #People with pets 1 + Pets FirstName LastName DOB PetNames PetType 2 + 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3 + 1 Steven Jones 04/04/74 Allie cat 4 + 0 Jane Doe 24/05/78 5 + 1 James Smith 20/10/80 Spot 6 + + Filter 2 - by regex expression matching [include]: '^\d+' (include lines that start with a number) + + 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3 + 1 Steven Jones 04/04/74 Allie cat 4 + 0 Jane Doe 24/05/78 5 + 1 James Smith 20/10/80 Spot 6 + + Filter 3 - append a line number column: + + 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3 1 + 1 Steven Jones 04/04/74 Allie cat 4 2 + 0 Jane Doe 24/05/78 5 3 + 1 James Smith 20/10/80 Spot 6 4 + + Filter 4 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format) + + 2 Paula Brown 1978-05-24 Rex,Fluff dog,cat 3 1 + 1 Steven Jones 1974-04-04 Allie cat 4 2 + 0 Jane Doe 1978-05-24 5 3 + 1 James Smith 1980-10-20 Spot 6 4 + + Filter 5 - normalize list columns[5,6]: + + 2 Paula Brown 1978-05-24 Rex dog 3 1 + 2 Paula Brown 1978-05-24 Fluff cat 3 1 + 1 Steven Jones 1974-04-04 Allie cat 4 2 + 0 Jane Doe 1978-05-24 5 3 + 1 James Smith 1980-10-20 Spot 6 4 + + Filter 6 - append a line number column: + + 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 + +]]> + </token> + + <token name="@QUERY_HELP@"> +<![CDATA[ + +For help in using SQLite_ see: http://www.sqlite.org/docs.html + +**NOTE:** input for SQLite dates input field must be in the format: *YYYY-MM-DD* for example: 2015-09-30 + +See: http://www.sqlite.org/lang_datefunc.html + +**Example** + + Given 2 tabular datasets: *customers* and *sales* + + Dataset *customers* + + Table name: "customers" + + Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone" + + =========== ========== ========== ===================== ========== ============ + #CustomerID FirstName LastName Email DOB Phone + =========== ========== ========== ===================== ========== ============ + 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222 + 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545 + 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232 + 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888 + =========== ========== ========== ===================== ========== ============ + + Dataset *sales* + + Table name: "sales" + + Column names: "CustomerID,Date,SaleAmount" + + ============= ============ ============ + #CustomerID Date SaleAmount + ============= ============ ============ + 2 2004-05-06 100.22 + 1 2004-05-07 99.95 + 3 2004-05-07 122.95 + 3 2004-05-13 100.00 + 4 2004-05-22 555.55 + ============= ============ ============ + + The query + + :: + + SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales" + FROM customers join sales on customers.CustomerID = sales.CustomerID + GROUP BY customers.CustomerID ORDER BY TotalSales DESC; + + Produces this tabular output: + + ========== ======== ========== + #FirstName LastName TotalSales + ========== ======== ========== + James Smith 555.55 + Paula Brown 222.95 + Steven Goldfish 100.22 + John Smith 99.95 + ========== ======== ========== + + + If the optional Table name and Column names inputs are not used, the query would be: + + :: + + SELECT t1.c2 as "FirstName", t1.c3 as "LastName", sum(t2.c3) as "TotalSales" + FROM t1 join t2 on t1.c1 = t2.c1 + GROUP BY t1.c1 ORDER BY TotalSales DESC; + + You can selectively name columns, e.g. on the customers input you could just name columns 2,3, and 5: + + Column names: ,FirstName,LastName,,BirthDate + + Results in the following data base table + + =========== ========== ========== ===================== ========== ============ + #c1 FirstName LastName c4 BirthDate c6 + =========== ========== ========== ===================== ========== ============ + 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222 + 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545 + 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232 + 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888 + =========== ========== ========== ===================== ========== ============ + + + Regular_expression_ functions are included for: + + :: + + matching: re_match('pattern',column) + + SELECT t1.FirstName, t1.LastName + FROM t1 + WHERE re_match('^.*\.(net|org)$',c4) + + Results: + + =========== ========== + #FirstName LastName + =========== ========== + Steven Goldfish + Paula Brown + =========== ========== + + + :: + + searching: re_search('pattern',column) + substituting: re_sub('pattern','replacement,column) + + SELECT t1.FirstName, t1.LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB" + FROM t1 + WHERE re_search('[hp]er',c4) + + Results: + + + =========== ========== ========== + #FirstName LastName DOB + =========== ========== ========== + Steven Goldfish 04/04/74 + Paula Brown 24/05/78 + James Smith 20/10/80 + =========== ========== ========== + +.. _Regular_expression: https://docs.python.org/release/2.7/library/re.html +.. _SQLite: http://www.sqlite.org/index.html +.. _SQLite_functions: http://www.sqlite.org/docs.html + + +]]> + </token> + +</macros> +