Mercurial > repos > iuc > sqlite_to_tabular

comparison macros.xml @ 13:c29d2f80a066 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
author iuc
date Thu, 19 Aug 2021 19:40:25 +0000
parents 575cd6cd537c
children f768f6183386
comparison
equal deleted inserted replaced
12:575cd6cd537c 13:c29d2f80a066
30 #set $filter_dict['action'] = str($fi.filter.regex_action) 30 #set $filter_dict['action'] = str($fi.filter.regex_action)
31 #silent $input_filters.append($filter_dict) 31 #silent $input_filters.append($filter_dict)
32 #elif $fi.filter.filter_type == 'select_columns': 32 #elif $fi.filter.filter_type == 'select_columns':
33 #set $filter_dict = dict() 33 #set $filter_dict = dict()
34 #set $filter_dict['filter'] = str($fi.filter.filter_type) 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(',')] 35 #set $filter_dict['columns'] = [int($c) for $c in str($fi.filter.columns).replace('c','').split(',')]
36 #silent $input_filters.append($filter_dict)
37 #elif $fi.filter.filter_type == 'select_column_slices':
38 #set $filter_dict = dict()
39 #set $filter_dict['filter'] = str($fi.filter.filter_type)
40 #set $filter_dict['columns'] = [$c for $c in str($fi.filter.columns).split(',')]
36 #silent $input_filters.append($filter_dict) 41 #silent $input_filters.append($filter_dict)
37 #elif $fi.filter.filter_type == 'replace': 42 #elif $fi.filter.filter_type == 'replace':
38 #set $filter_dict = dict() 43 #set $filter_dict = dict()
39 #set $filter_dict['filter'] = str($fi.filter.filter_type) 44 #set $filter_dict['filter'] = str($fi.filter.filter_type)
40 #set $filter_dict['column'] = int(str($fi.filter.column).replace('c','')) 45 #set $filter_dict['column'] = int(str($fi.filter.column).replace('c',''))
50 #silent $input_filters.append($filter_dict) 55 #silent $input_filters.append($filter_dict)
51 #elif str($fi.filter.filter_type).endswith('pend_text'): 56 #elif str($fi.filter.filter_type).endswith('pend_text'):
52 #set $filter_dict = dict() 57 #set $filter_dict = dict()
53 #set $filter_dict['filter'] = str($fi.filter.filter_type) 58 #set $filter_dict['filter'] = str($fi.filter.filter_type)
54 #set $filter_dict['column_text'] = str($fi.filter.column_text) 59 #set $filter_dict['column_text'] = str($fi.filter.column_text)
60 #silent $input_filters.append($filter_dict)
61 #elif str($fi.filter.filter_type).endswith('pend_dataset_name'):
62 #set $filter_dict = dict()
63 #set $filter_dict['filter'] = str($fi.filter.filter_type).replace('dataset_name', 'text')
64 #set $filter_dict['column_text'] = $dataset_name
55 #silent $input_filters.append($filter_dict) 65 #silent $input_filters.append($filter_dict)
56 #elif $fi.filter.filter_type == 'normalize': 66 #elif $fi.filter.filter_type == 'normalize':
57 #set $filter_dict = dict() 67 #set $filter_dict = dict()
58 #set $filter_dict['filter'] = str($fi.filter.filter_type) 68 #set $filter_dict['filter'] = str($fi.filter.filter_type)
59 #set $filter_dict['columns'] = [int(str($ci).replace('c','')) for $ci in str($fi.filter.columns).split(',')] 69 #set $filter_dict['columns'] = [int(str($ci).replace('c','')) for $ci in str($fi.filter.columns).split(',')]
127 <param name="filter_type" type="select" label="Filter By"> 137 <param name="filter_type" type="select" label="Filter By">
128 <option value="skip">skip leading lines</option> 138 <option value="skip">skip leading lines</option>
129 <option value="comment">comment char</option> 139 <option value="comment">comment char</option>
130 <option value="regex">by regex expression matching</option> 140 <option value="regex">by regex expression matching</option>
131 <option value="select_columns">select columns</option> 141 <option value="select_columns">select columns</option>
142 <option value="select_column_slices">select columns by indices/slices</option>
132 <option value="replace">regex replace value in column</option> 143 <option value="replace">regex replace value in column</option>
133 <option value="prepend_line_num">prepend a line number column</option> 144 <option value="prepend_line_num">prepend a line number column</option>
134 <option value="append_line_num">append a line number column</option> 145 <option value="append_line_num">append a line number column</option>
146 <option value="prepend_dataset_name">prepend a column with the dataset name</option>
147 <option value="append_dataset_name">append a column with the dataset name</option>
135 <option value="prepend_text">prepend a column with the given text</option> 148 <option value="prepend_text">prepend a column with the given text</option>
136 <option value="append_text">append a column with the given text</option> 149 <option value="append_text">append a column with the given text</option>
137 <option value="normalize">normalize list columns, replicates row for each item in list</option> 150 <option value="normalize">normalize list columns, replicates row for each item in list</option>
138 </param> 151 </param>
139 <when value="skip"> 152 <when value="skip">
145 <expand macro="comment_char_options" /> 158 <expand macro="comment_char_options" />
146 </param> 159 </param>
147 </when> 160 </when>
148 <when value="prepend_line_num"/> 161 <when value="prepend_line_num"/>
149 <when value="append_line_num"/> 162 <when value="append_line_num"/>
163 <when value="prepend_dataset_name"/>
164 <when value="append_dataset_name"/>
150 <when value="prepend_text"> 165 <when value="prepend_text">
151 <param name="column_text" type="text" value="" label="text for column"> 166 <param name="column_text" type="text" value="" label="text for column">
152 </param> 167 </param>
153 </when> 168 </when>
154 <when value="append_text"> 169 <when value="append_text">
170 <param name="columns" type="text" value="" label="enter column numbers to keep" 185 <param name="columns" type="text" value="" label="enter column numbers to keep"
171 help="example: 1,4,2 or c1,c4,c2(selects the first,fourth, and second columns)"> 186 help="example: 1,4,2 or c1,c4,c2(selects the first,fourth, and second columns)">
172 <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator> 187 <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator>
173 </param> 188 </param>
174 </when> 189 </when>
190 <when value="select_column_slices">
191 <param name="columns" type="text" value="" label="enter indices or slices of the columns to keep">
192 <help><![CDATA[ Python offset indexes or slices. Examples:
193 <ul>
194 <li>Column offset indexes: 0,3,1 (selects the first,fourth, and second columns)</li>
195 <li>Negative column numbers: -1,-2 (selects the last, and second last columns)</li>
196 <li>python slices ( slice(start, stop[, step]) select a range of columns): <li>
197 <ul>
198 <li>0:3 or :3 (selects the first 3 columns)</li>
199 <li>3:5 (selects the fourth and fifth columns)</li>
200 <li>2: (selects all columns after the second)</li>
201 <li>-2: (selects the last 2 columns)</li>
202 <li>2::-1 (selects the first 3 columns n reverse order: third,second,first)</li>
203 </ul>
204 </ul>
205 ]]></help>
206 <validator type="regex" message="Column ordinal positions separated by commas">^(-?[1-9]\d*|((-?\d+)?:(-?\d*(:-?\d*)?)))(,(-?[1-9]\d*|((-?\d+)?:(-?\d*(:-?\d*)?))))*$</validator>
207 </param>
208 </when>
209
175 <when value="replace"> 210 <when value="replace">
176 <param name="column" type="text" value="" label="enter column number to replace" 211 <param name="column" type="text" value="" label="enter column number to replace"
177 help="example: 1 or c1 (selects the first column)"> 212 help="example: 1 or c1 (selects the first column)">
178 <validator type="regex" message="Column ordinal position">^(c?[1-9]\d*)$</validator> 213 <validator type="regex" message="Column ordinal position">^(c?[1-9]\d*)$</validator>
179 </param> 214 </param>
209 244
210 <token name="@LINEFILTERS_HELP@"> 245 <token name="@LINEFILTERS_HELP@">
211 <![CDATA[ 246 <![CDATA[
212 **Input Line Filters** 247 **Input Line Filters**
213 248
214 As a tabular file is being read, line filters may be applied. 249 As a tabular file is being read, line filters may be applied:
215 250
216 :: 251 - skip leading lines - skip the first *number* of lines
217 252 - comment char - omit any lines that start with the specified comment character
218 - skip leading lines skip the first *number* of lines 253 - by regex expression matching - *include/exclude* lines that match the regex expression
219 - comment char omit any lines that start with the specified comment character 254 - select columns - choose to include only selected columns in the order specified
220 - by regex expression matching *include/exclude* lines the match the regex expression 255 - select columns by indices/slices - *indices or slices* of the columns to keep (python_list_ indexing)
221 - select columns choose to include only selected columns in the order specified 256 - regex replace value in column - replace a field in a column using a regex substitution (good for date reformatting)
222 - regex replace value in column replace a field in a column using a regex substitution (good for date reformatting) 257 - regex replace value in column - add a new column using a regex substitution of a column value
223 - regex replace value in column add a new column using a regex substitution of a column value 258 - prepend a line number column - each line has the *ordinal* value of the line read by this filter as the first column
224 - prepend a line number column each line has the ordinal value of the line read by this filter as the first column 259 - append a line number column - each line has the *ordinal* value of the line read by this filter as the last column
225 - append a line number column each line has the ordinal value of the line read by this filter as the last column 260 - prepend a text column - each line has the text string as the first column
226 - prepend a text column each line has the text string as the first column 261 - append a text column - each line has the text string as the last column
227 - append a text column each line has the text string as the last column 262 - prepend the dataset name - each line has the *dataset name* as the first column
228 - normalize list columns replicates the line for each item in the specified list *columns* 263 - append the dataset name - each line has the *dataset name* as the last column
264 - normalize list columns - replicates the line for each item in the specified list *columns*
265
266 .. _python_list: https://docs.python.org/3/library/stdtypes.html#common-sequence-operations
229 ]]> 267 ]]>
230 </token> 268 </token>
231 269
232 <token name="@LINEFILTERS_HELP_EXAMPLE@"> 270 <token name="@LINEFILTERS_HELP_EXAMPLE@">
233 <![CDATA[ 271 <![CDATA[
282 2 Paula Brown 1978-05-24 Fluff cat 3 1 320 2 Paula Brown 1978-05-24 Fluff cat 3 1
283 1 Steven Jones 1974-04-04 Allie cat 4 2 321 1 Steven Jones 1974-04-04 Allie cat 4 2
284 0 Jane Doe 1978-05-24 5 3 322 0 Jane Doe 1978-05-24 5 3
285 1 James Smith 1980-10-20 Spot 6 4 323 1 James Smith 1980-10-20 Spot 6 4
286 324
287 Filter 6 - append a line number column: 325 Filter 6 - select columns by indices/slices: '1:6'
288 326
289 2 Paula Brown 1978-05-24 Rex dog 3 1 1 327 Paula Brown 1978-05-24 Rex dog
290 2 Paula Brown 1978-05-24 Fluff cat 3 1 2 328 Paula Brown 1978-05-24 Fluff cat
291 1 Steven Jones 1974-04-04 Allie cat 4 2 3 329 Steven Jones 1974-04-04 Allie cat
292 0 Jane Doe 1978-05-24 5 3 4 330 Jane Doe 1978-05-24
293 1 James Smith 1980-10-20 Spot 6 4 5 331 James Smith 1980-10-20 Spot
294 332
295 ]]> 333 ]]>
296 </token> 334 </token>
297 335
298 <token name="@QUERY_HELP@"> 336 <token name="@QUERY_HELP@">