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comparison macros.xml @ 0:7ff05a1ffdd7 draft default tip

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:18:56 -0400
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-1:000000000000 0:7ff05a1ffdd7
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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>