Mercurial > repos > nml > csvtk_join
comparison macros.xml @ 0:31442b046269 draft default tip
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author | nml |
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date | Tue, 19 May 2020 17:22:35 -0400 |
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-1:000000000000 | 0:31442b046269 |
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1 <macros> | |
2 <token name="@VERSION@">0.20.0</token> | |
3 <token name="@GALAXY_VERSION@">galaxy0</token> | |
4 <xml name="requirements"> | |
5 <requirements> | |
6 <requirement type="package" version="@VERSION@">csvtk</requirement> | |
7 </requirements> | |
8 </xml> | |
9 <xml name="version_cmd"> | |
10 <version_command>csvtk version</version_command> | |
11 </xml> | |
12 <xml name="text_sanitizer"> | |
13 <sanitizer> | |
14 <valid initial="string.printable"> | |
15 <remove value="'"/> | |
16 </valid> | |
17 </sanitizer> | |
18 </xml> | |
19 <xml name="multi_input"> | |
20 <param type="data" name="in_1" format="csv,tabular" | |
21 multiple="true" optional="false" | |
22 label="Specify TSV or CSV file inputs" | |
23 help="Input tsv or csv files to analyze. HOWEVER, they must all be the **same file type** or the tool will fail/not give correct results!" | |
24 /> | |
25 </xml> | |
26 <xml name="singular_input"> | |
27 <param type="data" name="in_1" format="csv,tabular" | |
28 multiple="false" optional="false" | |
29 label="Specify an input TSV or CSV file" | |
30 help="Input a TSV or CSV file to work on" | |
31 /> | |
32 </xml> | |
33 <xml name="ignore_case"> | |
34 <param type="boolean" name="ignore_case" | |
35 falsevalue="" truevalue="-i" | |
36 checked="false" | |
37 argument="-i" | |
38 label="Ignore cell case?" | |
39 help="ABC == abc" | |
40 /> | |
41 </xml> | |
42 <xml name="global_parameters"> | |
43 <section name="global_param" title="csvtk Global Parameters" expanded="false"> | |
44 <param type="boolean" name="header" | |
45 falsevalue="-H" truevalue="" | |
46 checked="true" | |
47 argument="-H" | |
48 label="Input file has a header line" | |
49 /> | |
50 <param type="boolean" name="illegal_rows" | |
51 falsevalue="" truevalue="-I" | |
52 checked="false" | |
53 argument="-I" | |
54 label="Ignore illegal rows" | |
55 help="Use if file has illegal rows as defined in the help section" | |
56 /> | |
57 <param type="boolean" name="empty_rows" | |
58 falsevalue="" truevalue="-E" | |
59 checked="false" | |
60 argument="-E" | |
61 label="Ignore empty rows" | |
62 help="Ignore rows with no data (only needed if input has empty rows)" | |
63 /> | |
64 <param type="boolean" name="lazy_quotes" | |
65 falsevalue="" truevalue="-l" | |
66 checked="false" | |
67 argument="-l" | |
68 label="File has Lazy quotes" | |
69 help="(TSV files only) If Yes, a quote may appear in an unquoted field and a non-doubled quote may appear in a quoted field" | |
70 /> | |
71 </section> | |
72 </xml> | |
73 <xml name="fields_input"> | |
74 <conditional name="column_text" > | |
75 <param type="select" name="select" label="Select input column(s) based on" argument="-F -f"> | |
76 <option value="string">Column Name(s)</option> | |
77 <option value="column">Column Number(s)</option> | |
78 </param> | |
79 <when value="column"> | |
80 <param type="data_column" name="in_text" | |
81 data_ref="in_1" | |
82 multiple="true" | |
83 label="Input column number(s)" | |
84 help="Select column(s) to use for analysis" | |
85 /> | |
86 </when> | |
87 <when value="string"> | |
88 <param type="text" name="in_text" | |
89 optional="false" | |
90 label="Input column name(s)" | |
91 help="Multiple columns can be given if separated by a ' , '. | |
92 Column numbers can be given too - ex. '1,2' will target columns 1 and 2. | |
93 Please see the help section below for more detailed info"> | |
94 <sanitizer> | |
95 <valid initial="string.printable"> | |
96 <remove value="'"/> | |
97 </valid> | |
98 </sanitizer> | |
99 </param> | |
100 </when> | |
101 </conditional> | |
102 </xml> | |
103 <xml name="singular_fields_input"> | |
104 <conditional name="column_text" > | |
105 <param type="select" name="select" label="Select input column based on" argument="-f"> | |
106 <option value="string">Column Name</option> | |
107 <option value="column">Column Number</option> | |
108 </param> | |
109 <when value="column"> | |
110 <param type="data_column" name="in_text" | |
111 data_ref="in_1" | |
112 multiple="false" | |
113 label="Input column number" | |
114 help="Select column to use for analysis" | |
115 /> | |
116 </when> | |
117 <when value="string"> | |
118 <param type="text" name="in_text" | |
119 optional="false" | |
120 label="Input column name" | |
121 help="Input column name or number ex. 'Length' or '1'. | |
122 Please see the help section below for more detailed info"> | |
123 <sanitizer> | |
124 <valid initial="string.printable"> | |
125 <remove value="'"/> | |
126 </valid> | |
127 </sanitizer> | |
128 </param> | |
129 </when> | |
130 </conditional> | |
131 </xml> | |
132 <xml name="plot_field"> | |
133 <conditional name="column_text" > | |
134 <param type="select" name="select" label="Select input data column based on" argument="-f"> | |
135 <option value="string">Column Name</option> | |
136 <option value="column">Column Number</option> | |
137 </param> | |
138 <when value="column"> | |
139 <param type="data_column" name="in_text" | |
140 data_ref="in_1" | |
141 multiple="false" | |
142 label="Input data column number" | |
143 /> | |
144 </when> | |
145 <when value="string"> | |
146 <param type="text" name="in_text" | |
147 optional="false" | |
148 label="Input data column name" | |
149 help="Can use column name or column number"> | |
150 <sanitizer> | |
151 <valid initial="string.printable"> | |
152 <remove value="'"/> | |
153 </valid> | |
154 </sanitizer> | |
155 </param> | |
156 </when> | |
157 </conditional> | |
158 </xml> | |
159 <xml name="groups_input"> | |
160 <conditional name="group_field" > | |
161 <param type="select" name="select_group" label="Select column to group data" argument="-g" optional="false" help="Specify a single column that is used to create data groups. An example is shown in the help section"> | |
162 <option value="none">None</option> | |
163 <option value="string">Column Name</option> | |
164 <option value="column">Column Number</option> | |
165 </param> | |
166 <when value="none" /> | |
167 <when value="column"> | |
168 <param type="data_column" name="in_text" | |
169 data_ref="in_1" | |
170 multiple="false" | |
171 label="Group by column number" | |
172 /> | |
173 </when> | |
174 <when value="string"> | |
175 <param type="text" name="in_text" | |
176 optional="false" | |
177 label="Group by column name" | |
178 help="Can use column name or number"> | |
179 <sanitizer> | |
180 <valid initial="string.printable"> | |
181 <remove value="'"/> | |
182 </valid> | |
183 </sanitizer> | |
184 </param> | |
185 </when> | |
186 </conditional> | |
187 </xml> | |
188 <xml name="global_plot_parameters"> | |
189 <section name="plot_parameters" title="Advanced Optional Plot Parameters" expanded="false"> | |
190 <param type="float" name="figure_height" | |
191 argument="--height" | |
192 optional="true" | |
193 label="Figure Height (Default 4.5)" | |
194 /> | |
195 <param type="float" name="figure_width" | |
196 argument="--width" | |
197 optional="true" | |
198 label="Figure Width (Default 1.5)" | |
199 /> | |
200 <param type="float" name="tick_width" | |
201 argument="--tick-width" | |
202 optional="true" | |
203 label="Axis Tick Width (Default 1.5)" | |
204 /> | |
205 <param type="text" name="title" | |
206 argument="--title" | |
207 optional="true" | |
208 label="Specify Figure Title"> | |
209 <sanitizer> | |
210 <valid initial="string.printable"> | |
211 <remove value="'"/> | |
212 </valid> | |
213 </sanitizer> | |
214 </param> | |
215 <param type="text" name="x_label" | |
216 argument="--xlab" | |
217 optional="true" | |
218 label="Specify X-axis label"> | |
219 <sanitizer> | |
220 <valid initial="string.printable"> | |
221 <remove value="'"/> | |
222 </valid> | |
223 </sanitizer> | |
224 </param> | |
225 <param type="float" name="min_x" | |
226 argument="--x-min" | |
227 optional="true" | |
228 label="Minimum value of X-axis (float)" | |
229 /> | |
230 <param type="float" name="max_x" | |
231 argument="--x-max" | |
232 optional="true" | |
233 label="Maximum value of X-axis (float)" | |
234 /> | |
235 <param type="text" name="y_label" | |
236 argument="--ylab" | |
237 optional="true" | |
238 label="Specify Y-axis label"> | |
239 <sanitizer> | |
240 <valid initial="string.printable"> | |
241 <remove value="'"/> | |
242 </valid> | |
243 </sanitizer> | |
244 </param> | |
245 <param type="float" name="min_y" | |
246 argument="--y-min" | |
247 optional="true" | |
248 label="Minimum value of Y-axis (float)" | |
249 /> | |
250 <param type="float" name="max_y" | |
251 argument="--y-max" | |
252 optional="true" | |
253 label="Maximum value of Y-axis (float)" | |
254 /> | |
255 </section> | |
256 </xml> | |
257 <token name="@HELP_COLUMNS@"> | |
258 Column Name Input Help | |
259 ###################### | |
260 | |
261 - Multiple names can be given if separated by a ' , '. | |
262 | |
263 - ex. 'ID,Organism' would target the columns named ID and Organism for the function | |
264 | |
265 - Column names are case SeNsitive | |
266 | |
267 - Column numbers can also be given: | |
268 | |
269 -ex. '1,2,3' or '1-3' for inputting columns 1-3. | |
270 | |
271 - You can also specify all but unwanted column(s) with a ' - '. | |
272 | |
273 - ex. '-ID' would target all columns but the ID column | |
274 | |
275 ---- | |
276 </token> | |
277 <token name="@HELP_INPUT_DATA@"> | |
278 Input Data | |
279 ########## | |
280 | |
281 :: | |
282 | |
283 **Limitations of Input Data** | |
284 | |
285 1. The CSV parser requires all the lines have same number of fields/columns. | |
286 If your file has illegal rows, set the "Illegal Rows" parameter to "Yes" to pass your data through | |
287 Even lines with spaces will cause error. | |
288 Example bad table below. | |
289 | |
290 2. By default, csvtk thinks files have header rows. If your file does not, set global parameter | |
291 "Has Header Row" to "No" | |
292 | |
293 3. Column names should be unique and are case sensitive! | |
294 | |
295 4. Lines starting with "#" or "$" will be ignored, if in the header row | |
296 | |
297 5. If " exists in tab-delimited files, set Lazy quotes global parameter to "Yes" | |
298 | |
299 Example bad table: | |
300 | |
301 +--------+--------+--------+--------+ | |
302 | Head 1 | Head 2 | Head 3 | Head 3 | | |
303 +========+========+========+========+ | |
304 | 1 | 2 | 3 | | | |
305 +--------+--------+--------+--------+ | |
306 | this | will | | break | | |
307 +--------+--------+--------+--------+ | |
308 | |
309 Bad tables may work if both the "Ignore Illegal Rows" and "Ignore Empty Rows" global parameters are set to "Yes", | |
310 But there is no guarentee of that! | |
311 | |
312 ---- | |
313 </token> | |
314 <token name="@HELP_END_STATEMENT@"> | |
315 More Information | |
316 ################ | |
317 For information from the creators of csvtk, please visit their site at: https://bioinf.shenwei.me/csvtk/ | |
318 | |
319 Although be aware that some features may not be available and some small changes were made to work with Galaxy. | |
320 | |
321 **Notable changes from their documentation:** | |
322 | |
323 - Cannot specify multiple file header names (IE cannot use "name;username" as a valid column match) | |
324 | |
325 - No single quotes / apostrophes allowed in text inputs | |
326 </token> | |
327 <xml name="citations"> | |
328 <citations> | |
329 <citation type="bibtex">@ARTICLE{a1, | |
330 title = {csvtk - CSV/TSV Toolkit}, | |
331 author = {Wei Shen}, | |
332 url = {https://github.com/shenwei356/csvtk} | |
333 } | |
334 }</citation> | |
335 </citations> | |
336 </xml> | |
337 </macros> |