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comparison macros.xml @ 0:c866ec050312 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
author iuc
date Tue, 18 Jul 2017 09:06:16 -0400
parents
children 89d898454f1e
comparison
equal deleted inserted replaced
-1:000000000000 0:c866ec050312
1 <macros>
2 <token name="@LINEFILTERS@">
3 <![CDATA[
4 ## set linefilters to the
5 #set $input_filters = []
6 #for $fi in $linefilters:
7 #if $fi.filter.filter_type == 'skip':
8 #set $skip_lines = None
9 #if str($fi.filter.skip_lines) != '':
10 #set $skip_lines = int($fi.filter.skip_lines)
11 #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0:
12 #set $skip_lines = int($tbl.table.metadata.comment_lines)
13 #end if
14 #if $skip_lines is not None:
15 #set $filter_dict = dict()
16 #set $filter_dict['filter'] = str($fi.filter.filter_type)
17 #set $filter_dict['count'] = $skip_lines
18 #silent $input_filters.append($filter_dict)
19 #end if
20 #elif $fi.filter.filter_type == 'comment':
21 #set $filter_dict = dict()
22 #set $filter_dict['filter'] = 'regex'
23 #set $filter_dict['pattern'] = '^(%s).*$' % '|'.join([chr(int(x)).replace('|','[|]') for x in (str($fi.filter.comment_char)).split(',')])
24 #set $filter_dict['action'] = 'exclude_match'
25 #silent $input_filters.append($filter_dict)
26 #elif $fi.filter.filter_type == 'regex':
27 #set $filter_dict = dict()
28 #set $filter_dict['filter'] = str($fi.filter.filter_type)
29 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
30 #set $filter_dict['action'] = str($fi.filter.regex_action)
31 #silent $input_filters.append($filter_dict)
32 #elif $fi.filter.filter_type == 'select_columns':
33 #set $filter_dict = dict()
34 #set $filter_dict['filter'] = str($fi.filter.filter_type)
35 #set $filter_dict['columns'] = [int(str($ci).replace('c','')) for $ci in str($fi.filter.columns).split(',')]
36 #silent $input_filters.append($filter_dict)
37 #elif $fi.filter.filter_type == 'replace':
38 #set $filter_dict = dict()
39 #set $filter_dict['filter'] = str($fi.filter.filter_type)
40 #set $filter_dict['column'] = int(str($fi.filter.column).replace('c',''))
41 #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
42 #set $filter_dict['replace'] = str($fi.filter.regex_replace)
43 #silent $input_filters.append($filter_dict)
44 #elif str($fi.filter.filter_type).endswith('pend_line_num'):
45 #set $filter_dict = dict()
46 #set $filter_dict['filter'] = str($fi.filter.filter_type)
47 #silent $input_filters.append($filter_dict)
48 #elif str($fi.filter.filter_type).endswith('pend_text'):
49 #set $filter_dict = dict()
50 #set $filter_dict['filter'] = str($fi.filter.filter_type)
51 #set $filter_dict['column_text'] = str($fi.filter.column_text)
52 #silent $input_filters.append($filter_dict)
53 #elif $fi.filter.filter_type == 'normalize':
54 #set $filter_dict = dict()
55 #set $filter_dict['filter'] = str($fi.filter.filter_type)
56 #set $filter_dict['columns'] = [int(str($ci).replace('c','')) for $ci in str($fi.filter.columns).split(',')]
57 #set $filter_dict['separator'] = str($fi.filter.separator)
58 #silent $input_filters.append($filter_dict)
59 #end if
60 #end for
61 ]]>
62 </token>
63 <xml name="macro_line_filters">
64 <repeat name="linefilters" title="Filter Tabular Input Lines">
65 <conditional name="filter">
66 <param name="filter_type" type="select" label="Filter By">
67 <option value="skip">skip leading lines</option>
68 <option value="comment">comment char</option>
69 <option value="regex">by regex expression matching</option>
70 <option value="select_columns">select columns</option>
71 <option value="replace">regex replace value in column</option>
72 <option value="prepend_line_num">prepend a line number column</option>
73 <option value="append_line_num">append a line number column</option>
74 <option value="prepend_text">prepend a column with the given text</option>
75 <option value="append_text">append a column with the given text</option>
76 <option value="normalize">normalize list columns, replicates row for each item in list</option>
77 </param>
78 <when value="skip">
79 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines"
80 help="Leave blank to use the comment lines metadata for this dataset" />
81 </when>
82 <when value="comment">
83 <param name="comment_char" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are skipped">
84 <option value="62">&gt;</option>
85 <option value="64">@</option>
86 <option value="43">+</option>
87 <option value="60">&lt;</option>
88 <option value="42">*</option>
89 <option value="45">-</option>
90 <option value="61">=</option>
91 <option value="124">|</option>
92 <option value="63">?</option>
93 <option value="36">$</option>
94 <option value="46">.</option>
95 <option value="58">:</option>
96 <option value="38">&amp;</option>
97 <option value="37">%</option>
98 <option value="94">^</option>
99 <option value="35">&#35;</option>
100 <option value="33">!</option>
101 </param>
102 </when>
103 <when value="prepend_line_num"/>
104 <when value="append_line_num"/>
105 <when value="prepend_text">
106 <param name="column_text" type="text" value="" label="text for column">
107 </param>
108 </when>
109 <when value="append_text">
110 <param name="column_text" type="text" value="" label="text for column">
111 </param>
112 </when>
113 <when value="regex">
114 <param name="regex_pattern" type="text" value="" label="regex pattern">
115 <sanitizer sanitize="False"/>
116 </param>
117 <param name="regex_action" type="select" label="action for regex match">
118 <option value="exclude_match">exclude line on pattern match</option>
119 <option value="include_match">include line on pattern match</option>
120 <option value="exclude_find">exclude line if pattern found</option>
121 <option value="include_find">include line if pattern found</option>
122 </param>
123 </when>
124 <when value="select_columns">
125 <param name="columns" type="text" value="" label="enter column numbers to keep"
126 help="example: 1,4,2 or c1,c4,c2(selects the first,fourth, and second columns)">
127 <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator>
128 </param>
129 </when>
130 <when value="replace">
131 <param name="column" type="text" value="" label="enter column number to replace"
132 help="example: 1 or c1 (selects the first column)">
133 <validator type="regex" message="Column ordinal position separated by commas">^(c?[1-9]\d*)$</validator>
134 </param>
135 <param name="regex_pattern" type="text" value="" label="regex pattern">
136 <sanitizer sanitize="False"/>
137 </param>
138 <param name="regex_replace" type="text" value="" label="replacement expression">
139 <sanitizer sanitize="False"/>
140 </param>
141 </when>
142 <when value="normalize">
143 <param name="columns" type="text" value="" label="enter column numbers to normalize">
144 <help><![CDATA[
145 example: 2,4 or c2,c4 (selects the second, and fourth columns)
146 If multiple columns are selected, they should have the same length and separator on each line
147 ]]></help>
148 <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator>
149 </param>
150 <param name="separator" type="text" value="," label="List item delimiter in column">
151 <sanitizer sanitize="False"/>
152 <validator type="regex" message="Anything but TAB or Newline">^[^\t\n\r\f\v]+$</validator>
153 </param>
154 </when>
155 </conditional>
156 </repeat>
157 </xml>
158
159 <token name="@LINEFILTERS_HELP@">
160 <![CDATA[
161 **Input Line Filters**
162
163 As a tabular file is being read, line filters may be applied.
164
165 ::
166
167 - skip leading lines skip the first *number* of lines
168 - comment char omit any lines that start with the specified comment character
169 - by regex expression matching *include/exclude* lines the match the regex expression
170 - select columns choose to include only selected columns in the order specified
171 - regex replace value in column replace a field in a column using a regex substitution (good for date reformatting)
172 - prepend a line number column each line has the ordinal value of the line read by this filter as the first column
173 - append a line number column each line has the ordinal value of the line read by this filter as the last column
174 - prepend a text column each line has the text string as the first column
175 - append a text column each line has the text string as the last column
176 - normalize list columns replicates the line for each item in the specified list *columns*
177 ]]>
178 </token>
179
180 <token name="@LINEFILTERS_HELP_EXAMPLE@">
181 <![CDATA[
182 **Line Filtering Example**
183 *(Six filters are applied as the following file is read)*
184
185 ::
186
187 Input Tabular File:
188
189 #People with pets
190 Pets FirstName LastName DOB PetNames PetType
191 2 Paula Brown 24/05/78 Rex,Fluff dog,cat
192 1 Steven Jones 04/04/74 Allie cat
193 0 Jane Doe 24/05/78
194 1 James Smith 20/10/80 Spot
195
196
197 Filter 1 - append a line number column:
198
199 #People with pets 1
200 Pets FirstName LastName DOB PetNames PetType 2
201 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3
202 1 Steven Jones 04/04/74 Allie cat 4
203 0 Jane Doe 24/05/78 5
204 1 James Smith 20/10/80 Spot 6
205
206 Filter 2 - by regex expression matching [include]: '^\d+' (include lines that start with a number)
207
208 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3
209 1 Steven Jones 04/04/74 Allie cat 4
210 0 Jane Doe 24/05/78 5
211 1 James Smith 20/10/80 Spot 6
212
213 Filter 3 - append a line number column:
214
215 2 Paula Brown 24/05/78 Rex,Fluff dog,cat 3 1
216 1 Steven Jones 04/04/74 Allie cat 4 2
217 0 Jane Doe 24/05/78 5 3
218 1 James Smith 20/10/80 Spot 6 4
219
220 Filter 4 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format)
221
222 2 Paula Brown 1978-05-24 Rex,Fluff dog,cat 3 1
223 1 Steven Jones 1974-04-04 Allie cat 4 2
224 0 Jane Doe 1978-05-24 5 3
225 1 James Smith 1980-10-20 Spot 6 4
226
227 Filter 5 - normalize list columns[5,6]:
228
229 2 Paula Brown 1978-05-24 Rex dog 3 1
230 2 Paula Brown 1978-05-24 Fluff cat 3 1
231 1 Steven Jones 1974-04-04 Allie cat 4 2
232 0 Jane Doe 1978-05-24 5 3
233 1 James Smith 1980-10-20 Spot 6 4
234
235 Filter 6 - append a line number column:
236
237 2 Paula Brown 1978-05-24 Rex dog 3 1 1
238 2 Paula Brown 1978-05-24 Fluff cat 3 1 2
239 1 Steven Jones 1974-04-04 Allie cat 4 2 3
240 0 Jane Doe 1978-05-24 5 3 4
241 1 James Smith 1980-10-20 Spot 6 4 5
242
243 ]]>
244 </token>
245
246 <token name="@QUERY_HELP@">
247 <![CDATA[
248
249 For help in using SQLite_ see: http://www.sqlite.org/docs.html
250
251 **NOTE:** input for SQLite dates input field must be in the format: *YYYY-MM-DD* for example: 2015-09-30
252
253 See: http://www.sqlite.org/lang_datefunc.html
254
255 **Example**
256
257 Given 2 tabular datasets: *customers* and *sales*
258
259 Dataset *customers*
260
261 Table name: "customers"
262
263 Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone"
264
265 =========== ========== ========== ===================== ========== ============
266 #CustomerID FirstName LastName Email DOB Phone
267 =========== ========== ========== ===================== ========== ============
268 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
269 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
270 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
271 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
272 =========== ========== ========== ===================== ========== ============
273
274 Dataset *sales*
275
276 Table name: "sales"
277
278 Column names: "CustomerID,Date,SaleAmount"
279
280 ============= ============ ============
281 #CustomerID Date SaleAmount
282 ============= ============ ============
283 2 2004-05-06 100.22
284 1 2004-05-07 99.95
285 3 2004-05-07 122.95
286 3 2004-05-13 100.00
287 4 2004-05-22 555.55
288 ============= ============ ============
289
290 The query
291
292 ::
293
294 SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales"
295 FROM customers join sales on customers.CustomerID = sales.CustomerID
296 GROUP BY customers.CustomerID ORDER BY TotalSales DESC;
297
298 Produces this tabular output:
299
300 ========== ======== ==========
301 #FirstName LastName TotalSales
302 ========== ======== ==========
303 James Smith 555.55
304 Paula Brown 222.95
305 Steven Goldfish 100.22
306 John Smith 99.95
307 ========== ======== ==========
308
309
310 If the optional Table name and Column names inputs are not used, the query would be:
311
312 ::
313
314 SELECT t1.c2 as "FirstName", t1.c3 as "LastName", sum(t2.c3) as "TotalSales"
315 FROM t1 join t2 on t1.c1 = t2.c1
316 GROUP BY t1.c1 ORDER BY TotalSales DESC;
317
318 You can selectively name columns, e.g. on the customers input you could just name columns 2,3, and 5:
319
320 Column names: ,FirstName,LastName,,BirthDate
321
322 Results in the following data base table
323
324 =========== ========== ========== ===================== ========== ============
325 #c1 FirstName LastName c4 BirthDate c6
326 =========== ========== ========== ===================== ========== ============
327 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222
328 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545
329 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232
330 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888
331 =========== ========== ========== ===================== ========== ============
332
333
334 Regular_expression_ functions are included for:
335
336 ::
337
338 matching: re_match('pattern',column)
339
340 SELECT t1.FirstName, t1.LastName
341 FROM t1
342 WHERE re_match('^.*\.(net|org)$',c4)
343
344 Results:
345
346 =========== ==========
347 #FirstName LastName
348 =========== ==========
349 Steven Goldfish
350 Paula Brown
351 =========== ==========
352
353
354 ::
355
356 searching: re_search('pattern',column)
357 substituting: re_sub('pattern','replacement,column)
358
359 SELECT t1.FirstName, t1.LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB"
360 FROM t1
361 WHERE re_search('[hp]er',c4)
362
363 Results:
364
365
366 =========== ========== ==========
367 #FirstName LastName DOB
368 =========== ========== ==========
369 Steven Goldfish 04/04/74
370 Paula Brown 24/05/78
371 James Smith 20/10/80
372 =========== ========== ==========
373
374 .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html
375 .. _SQLite: http://www.sqlite.org/index.html
376 .. _SQLite_functions: http://www.sqlite.org/docs.html
377
378
379 ]]>
380 </token>
381
382 </macros>
383