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comparison pick_value.xml @ 0:bf793b71559a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value commit ef564483fa8dc267c599af8745aab4e03b0c57e0
author iuc
date Tue, 07 Nov 2023 09:02:42 +0000
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children b19e21af9c52
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-1:000000000000 0:bf793b71559a
1 <tool name="Pick parameter value" id="pick_value" version="0.1.0" profile="21.01" tool_type="expression">
2 <macros>
3 <xml name="booleans">
4 <repeat name="pick_from" title="Pick from">
5 <param name="value" type="boolean" optional="true" label="Value" />
6 </repeat>
7 </xml>
8 <xml name="integers">
9 <repeat name="pick_from" title="Pick from">
10 <param name="value" type="integer" label="Value" optional="true" />
11 </repeat>
12 </xml>
13 <xml name="floats">
14 <repeat name="pick_from" title="Pick from">
15 <param name="value" type="float" label="Value" optional="true" />
16 </repeat>
17 </xml>
18 <xml name="texts">
19 <repeat name="pick_from" title="Pick from">
20 <param name="value" type="text" optional="true" label="Value" />
21 </repeat>
22 </xml>
23 <xml name="datas">
24 <repeat name="pick_from" title="Pick from">
25 <param name="value" type="data" format="data" optional="true" label="Value" />
26 </repeat>
27 </xml>
28 <xml name="param_type">
29 <param name="param_type" type="select" label="Select type of parameter to select from">
30 <option value="data">Dataset</option>
31 <option value="text">Text</option>
32 <option value="integer">Integer</option>
33 <option value="float">Float</option>
34 <option value="boolean">Boolean</option>
35 </param>
36 </xml>
37 <xml name="param_pick_style">
38 <param name="pick_style" type="select" label="Picking behavior" help="How should the case when not exactly one value is non-null be handled?">
39 <option value="first">Pick first value</option>
40 <option value="first_or_default">Pick first value (or provide default)</option>
41 <option value="first_or_error">Pick first value (or fail)</option>
42 <option value="only">Pick only value</option>
43 </param>
44 </xml>
45 <xml name="type_conditional">
46 <conditional name="type_cond">
47 <expand macro="param_type" />
48 <when value="text">
49 <expand macro="texts" />
50 </when>
51 <when value="integer">
52 <expand macro="integers" />
53 </when>
54 <when value="float">
55 <expand macro="floats" />
56 </when>
57 <when value="boolean">
58 <expand macro="booleans" />
59 </when>
60 <when value="data">
61 <expand macro="datas" />
62 </when>
63 </conditional>
64 </xml>
65 <xml name="type_conditional_with_default">
66 <conditional name="type_cond">
67 <expand macro="param_type" />
68 <when value="text">
69 <expand macro="texts" />
70 <param name="default_value" type="text" label="Default Value" />
71 </when>
72 <when value="integer">
73 <expand macro="integers" />
74 <param name="default_value" type="integer" optional="true" label="Default Value" />
75 </when>
76 <when value="float">
77 <expand macro="floats" />
78 <param name="default_value" type="float" optional="true" label="Default Value" />
79 </when>
80 <when value="boolean">
81 <expand macro="booleans" />
82 <param name="default_value" type="boolean" label="Default Value" />
83 </when>
84 <when value="data">
85 <expand macro="datas" />
86 <param name="default_value" type="data" format="data" label="Default Value" />
87 </when>
88 </conditional>
89 </xml>
90 <xml name="style_conditional">
91 <conditional name="style_cond">
92 <expand macro="param_pick_style" />
93 <when value="first">
94 <expand macro="type_conditional" />
95 </when>
96 <when value="first_or_default">
97 <expand macro="type_conditional_with_default" />
98 </when>
99 <when value="first_or_error">
100 <expand macro="type_conditional" />
101 </when>
102 <when value="only">
103 <expand macro="type_conditional" />
104 </when>
105 </conditional>
106 </xml>
107 </macros>
108 <expression type="ecma5.1"><![CDATA[{
109 var out = null;
110 var pickStyle = $job.style_cond.pick_style;
111 var paramType = $job.style_cond.type_cond.param_type;
112 var pickFrom = $job.style_cond.type_cond.pick_from;
113 for ( var i = 0; i < pickFrom.length; i++ ) {
114 if ( pickFrom[i].value !== null ) {
115 if ( pickStyle == 'only' && out !== null ) {
116 return { '__error_message': 'Multiple null values found, only one allowed.' };
117 } else if ( out == null ) {
118 out = pickFrom[i].value;
119 }
120 }
121 }
122 if ( out == null && pickStyle == 'first_or_default' ) {
123 out = $job.style_cond.type_cond.default_value;
124 }
125 if ( paramType == "data" && out ) {
126 out = out.src;
127 }
128 if ( out == null && ( pickStyle == "first_or_error" || pickStyle == "only" ) ) {
129 return { '__error_message': 'No non-null values found among tool inputs.' };
130 }
131 return { 'output': out };
132 }]]></expression>
133 <inputs>
134 <expand macro="style_conditional" />
135 </inputs>
136 <outputs>
137 <output type="text" name="text_param" from="output">
138 <filter>style_cond['type_cond']['param_type'] == 'text'</filter>
139 </output>
140 <output type="integer" name="integer_param" from="output">
141 <filter>style_cond['type_cond']['param_type'] == 'integer'</filter>
142 </output>
143 <output type="float" name="float_param" from="output">
144 <filter>style_cond['type_cond']['param_type'] == 'float'</filter>
145 </output>
146 <output type="boolean" name="boolean_param" from="output">
147 <filter>style_cond['type_cond']['param_type'] == 'boolean'</filter>
148 </output>
149 <output type="data" name="data_param" from="output">
150 <filter>style_cond['type_cond']['param_type'] == 'data'</filter>
151 </output>
152 </outputs>
153 <help>
154 A "null" value is an empty value, it means some input wasn't specified or some tool produced
155 an empty value or was skipped entirely. This can be thought of as an NA in Excel or a None value
156 in Python. This expression tool can be fed multiple values - from parameter inputs or the
157 outputs or other tools or workflows - and pick one. This allows building workflows which can
158 skip steps and branch in complex ways.
159
160 There are subtle but important distinctions between the selection style - though they all
161 essentially pick the first value that is non-null (i.e. the first input with a real value).
162
163 - "Pick first value" is the default and will just return its own null value if none of the inputs
164 are non-null.
165 - "Pick first value (or provide default)" allows picking a default value that will be used if none of the
166 inputs are non-null.
167 - "Pick first value (or fail)" will cause the tool execution to fail if none of the selections are
168 non-null. This can be important because it provides a clearer indication that something went
169 wrong and can prevent the further evaluation of a workflow.
170 - "Pick only value" is like "First value (or fail)" in that it will cause an error if none of the
171 inputs are non-null but it will go further to ensure that exactly one value is non-null. When
172 building conditonal paths through a workflow this can ensure that at most one path is
173 taken.
174 </help>
175 <tests>
176 <test expect_num_outputs="1">
177 <conditional name="style_cond">
178 <param name="pick_style" value="first" />
179 <conditional name="type_cond">
180 <param name="param_type" value="data" />
181 <repeat name="pick_from">
182 <param name="value" value_json="null" />
183 </repeat>
184 <repeat name="pick_from">
185 <param name="value" value_json="null" />
186 </repeat>
187 <repeat name="pick_from">
188 <param name="value" value="simple_line.txt" />
189 </repeat>
190 <repeat name="pick_from">
191 <param name="value" value="simple_line_alternative.txt" />
192 </repeat>
193 </conditional>
194 </conditional>
195 <output name="data_param" value="simple_line.txt" />
196 </test>
197 <test expect_num_outputs="1">
198 <conditional name="style_cond">
199 <param name="pick_style" value="first" />
200 <conditional name="type_cond">
201 <param name="param_type" value="boolean" />
202 <repeat name="pick_from">
203 <param name="value" value_json="true" />
204 </repeat>
205 </conditional>
206 </conditional>
207 <output name="boolean_param" value_json="true" />
208 </test>
209 <test expect_num_outputs="1">
210 <conditional name="style_cond">
211 <param name="pick_style" value="first" />
212 <conditional name="type_cond">
213 <param name="param_type" value="boolean" />
214 <repeat name="pick_from">
215 <param name="value" value_json="null" />
216 </repeat>
217 <repeat name="pick_from">
218 <param name="value" value_json="true" />
219 </repeat>
220 </conditional>
221 </conditional>
222 <output name="boolean_param" value_json="true" />
223 </test>
224 <test expect_num_outputs="1">
225 <conditional name="style_cond">
226 <param name="pick_style" value="first" />
227 <conditional name="type_cond">
228 <param name="param_type" value="boolean" />
229 <repeat name="pick_from">
230 <param name="value" value_json="false" />
231 </repeat>
232 </conditional>
233 </conditional>
234 <output name="boolean_param" value_json="false" />
235 </test>
236 <test expect_num_outputs="1">
237 <conditional name="style_cond">
238 <param name="pick_style" value="first" />
239 <conditional name="type_cond">
240 <param name="param_type" value="boolean" />
241 <repeat name="pick_from">
242 <param name="value" value_json="null" />
243 </repeat>
244 <repeat name="pick_from">
245 <param name="value" value_json="false" />
246 </repeat>
247 <repeat name="pick_from">
248 <param name="value" value_json="true" />
249 </repeat>
250 </conditional>
251 </conditional>
252 <output name="boolean_param" value_json="false" />
253 </test>
254 <test expect_num_outputs="1">
255 <conditional name="style_cond">
256 <param name="pick_style" value="first" />
257 <conditional name="type_cond">
258 <param name="param_type" value="boolean" />
259 <repeat name="pick_from">
260 <param name="value" value_json="null" />
261 </repeat>
262 <repeat name="pick_from">
263 <param name="value" value_json="true" />
264 </repeat>
265 <repeat name="pick_from">
266 <param name="value" value_json="false" />
267 </repeat>
268 </conditional>
269 </conditional>
270 <output name="boolean_param" value_json="true" />
271 </test>
272 <test expect_failure="true">
273 <conditional name="style_cond">
274 <param name="pick_style" value="only" />
275 <conditional name="type_cond">
276 <param name="param_type" value="boolean" />
277 <repeat name="pick_from">
278 <param name="value" value_json="true" />
279 </repeat>
280 <repeat name="pick_from">
281 <param name="value" value_json="false" />
282 </repeat>
283 </conditional>
284 </conditional>
285 </test>
286 <test expect_failure="true">
287 <conditional name="style_cond">
288 <param name="pick_style" value="first_or_error" />
289 <conditional name="type_cond">
290 <param name="param_type" value="boolean" />
291 <repeat name="pick_from">
292 <param name="value" value_json="null" />
293 </repeat>
294 <repeat name="pick_from">
295 <param name="value" value_json="null" />
296 </repeat>
297 </conditional>
298 </conditional>
299 </test>
300 <test expect_failure="true">
301 <conditional name="style_cond">
302 <param name="pick_style" value="only" />
303 <conditional name="type_cond">
304 <param name="param_type" value="boolean" />
305 <repeat name="pick_from">
306 <param name="value" value_json="null" />
307 </repeat>
308 <repeat name="pick_from">
309 <param name="value" value_json="null" />
310 </repeat>
311 </conditional>
312 </conditional>
313 </test>
314 <test expect_num_outputs="1">
315 <conditional name="style_cond">
316 <param name="pick_style" value="first" />
317 <conditional name="type_cond">
318 <param name="param_type" value="boolean" />
319 <repeat name="pick_from">
320 <param name="value" value_json="null" />
321 </repeat>
322 </conditional>
323 </conditional>
324 <output name="boolean_param" value_json="null" />
325 </test>
326 <test expect_num_outputs="1">
327 <conditional name="style_cond">
328 <param name="pick_style" value="first_or_default" />
329 <conditional name="type_cond">
330 <param name="param_type" value="boolean" />
331 <repeat name="pick_from">
332 <param name="value" value_json="null" />
333 </repeat>
334 <param name="default_value" value_json="true" />
335 </conditional>
336 </conditional>
337 <output name="boolean_param" value_json="true" />
338 </test>
339 <test expect_num_outputs="1">
340 <conditional name="style_cond">
341 <param name="pick_style" value="first_or_default" />
342 <conditional name="type_cond">
343 <param name="param_type" value="boolean" />
344 <repeat name="pick_from">
345 <param name="value" value_json="null" />
346 </repeat>
347 <repeat name="pick_from">
348 <param name="value" value_json="null" />
349 </repeat>
350 <param name="default_value" value_json="false" />
351 </conditional>
352 </conditional>
353 <output name="boolean_param" value_json="false" />
354 </test>
355 <test expect_num_outputs="1">
356 <conditional name="style_cond">
357 <param name="pick_style" value="first_or_default" />
358 <conditional name="type_cond">
359 <param name="param_type" value="data" />
360 <repeat name="pick_from">
361 <param name="value" value_json="null" />
362 </repeat>
363 <repeat name="pick_from">
364 <param name="value" value_json="null" />
365 </repeat>
366 <param name="default_value" value="simple_line.txt" />
367 </conditional>
368 </conditional>
369 <output name="data_param" value="simple_line.txt" />
370 </test>
371 </tests>
372 </tool>
373