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comparison iedb_api.xml @ 6:8c6526a46319 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api commit 69cdfd826c760c5b091703919ddaee9c9f90d530
author iuc
date Sun, 23 Nov 2025 16:19:36 +0000
parents 1911ec100221
children
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5:1911ec100221 6:8c6526a46319
1 <tool id="iedb_api" name="IEDB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="iedb_api" name="IEDB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>MHC Binding prediction</description> 2 <description>MHC Binding prediction</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.15.3</token> 4 <token name="@TOOL_VERSION@">2.15.3</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 <token name="@PROFILE@">24.2</token> 6 <token name="@PROFILE@">24.2</token>
7 <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples=""> 7 <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples="">
8 <conditional name="alleles"> 8 <conditional name="alleles">
9 <param name="allelesrc" type="select" label="Alleles"> 9 <param name="allelesrc" type="select" label="Alleles">
10 <option value="history">From history</option> 10 <option value="history">From history</option>
106 <option value="smm">smm</option> 106 <option value="smm">smm</option>
107 <option value="comblib_sidney2008">comblib_sidney2008</option> 107 <option value="comblib_sidney2008">comblib_sidney2008</option>
108 <option value="netmhccons">netmhccons</option> 108 <option value="netmhccons">netmhccons</option>
109 <option value="pickpocket">pickpocket</option> 109 <option value="pickpocket">pickpocket</option>
110 </param> 110 </param>
111 <expand macro="alleles" hla_regex="(HLA-[A-CEG]\*[0-8][[0-9]:[0-9][0-9][0-9]*|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-5]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/> 111 <expand macro="alleles" hla_regex="(HLA-[A-CEG]\*[0-8][0-9]:[0-9][0-9][0-9]*|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-5]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/>
112 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> 112 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
113 <help>Used for any alleles which don't include specified lengths</help> 113 <help>Used for any alleles which don't include specified lengths</help>
114 <option value="8" selected="true">8</option> 114 <option value="8" selected="true">8</option>
115 <option value="9">9</option> 115 <option value="9">9</option>
116 <option value="10">10</option> 116 <option value="10">10</option>
170 </param> 170 </param>
171 <param name="proteasome" type="select" label="proteasome type"> 171 <param name="proteasome" type="select" label="proteasome type">
172 <option value="immuno">immuno</option> 172 <option value="immuno">immuno</option>
173 <option value="constitutive">constitutive</option> 173 <option value="constitutive">constitutive</option>
174 </param> 174 </param>
175 <expand macro="alleles" hla_regex="(HLA-[A-CE]\*[0-8][[0-9]:[0-9][0-9]|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-4]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/> 175 <expand macro="alleles" hla_regex="(HLA-[A-CE]\*[0-8][0-9]:[0-9][0-9]|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-4]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/>
176 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> 176 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
177 <help>Used for any alleles which don't include specified lengths</help> 177 <help>Used for any alleles which don't include specified lengths</help>
178 <option value="8" selected="true">8</option> 178 <option value="8" selected="true">8</option>
179 <option value="9">9</option> 179 <option value="9">9</option>
180 <option value="10">10</option> 180 <option value="10">10</option>
234 <!-- 234 <!--
235 <data name="output" format="tabular"/> 235 <data name="output" format="tabular"/>
236 --> 236 -->
237 <data name="output" format="tabular" label="IEDB ${prediction.tool} ${prediction.method}"/> 237 <data name="output" format="tabular" label="IEDB ${prediction.tool} ${prediction.method}"/>
238 <data name="output2" format="tabular" label="IEDB ${prediction.tool} ${prediction.method} residue scores" from_work_dir="iedb_results2"> 238 <data name="output2" format="tabular" label="IEDB ${prediction.tool} ${prediction.method} residue scores" from_work_dir="iedb_results2">
239 <filter>prediction['method'].startswith('Bepipred')</filter> 239 <filter>prediction['method'] == 'Bepipred'</filter>
240 </data> 240 </data>
241 </outputs> 241 </outputs>
242 <tests> 242 <tests>
243 <!-- test1 --> 243 <!-- test1 -->
244 <test> 244 <test expect_num_outputs="1">
245 <conditional name="prediction"> 245 <conditional name="prediction">
246 <param name="tool" value="mhci"/> 246 <param name="tool" value="mhci"/>
247 <param name="method" value="recommended"/> 247 <param name="method" value="recommended"/>
248 <conditional name="alleles"> 248 <conditional name="alleles">
249 <param name="allelesrc" value="entry"/> 249 <param name="allelesrc" value="entry"/>
259 <has_text text="LYNTVATLY" /> 259 <has_text text="LYNTVATLY" />
260 </assert_contents> 260 </assert_contents>
261 </output> 261 </output>
262 </test> 262 </test>
263 <!-- test2 --> 263 <!-- test2 -->
264 <test> 264 <test expect_num_outputs="1">
265 <conditional name="prediction"> 265 <conditional name="prediction">
266 <param name="tool" value="mhci"/> 266 <param name="tool" value="mhci"/>
267 <param name="method" value="recommended"/> 267 <param name="method" value="recommended"/>
268 <conditional name="alleles"> 268 <conditional name="alleles">
269 <param name="allelesrc" value="history"/> 269 <param name="allelesrc" value="history"/>
280 <has_text text="HKVPRRLLK" /> 280 <has_text text="HKVPRRLLK" />
281 </assert_contents> 281 </assert_contents>
282 </output> 282 </output>
283 </test> 283 </test>
284 <!-- test3 --> 284 <!-- test3 -->
285 <test> 285 <test expect_num_outputs="1">
286 <conditional name="prediction"> 286 <conditional name="prediction">
287 <param name="tool" value="mhci"/> 287 <param name="tool" value="mhci"/>
288 <param name="method" value="recommended"/> 288 <param name="method" value="recommended"/>
289 <conditional name="alleles"> 289 <conditional name="alleles">
290 <param name="allelesrc" value="history"/> 290 <param name="allelesrc" value="history"/>
304 <has_text text="HKVPRRLLK" /> 304 <has_text text="HKVPRRLLK" />
305 </assert_contents> 305 </assert_contents>
306 </output> 306 </output>
307 </test> 307 </test>
308 <!-- test4 --> 308 <!-- test4 -->
309 <test> 309 <test expect_num_outputs="1">
310 <conditional name="prediction"> 310 <conditional name="prediction">
311 <param name="tool" value="mhcii"/> 311 <param name="tool" value="mhcii"/>
312 <param name="method" value="recommended"/> 312 <param name="method" value="recommended"/>
313 <conditional name="alleles"> 313 <conditional name="alleles">
314 <param name="allelesrc" value="entry"/> 314 <param name="allelesrc" value="entry"/>
325 <has_text text="VATLYCVHQ" /> 325 <has_text text="VATLYCVHQ" />
326 </assert_contents> 326 </assert_contents>
327 </output> 327 </output>
328 </test> 328 </test>
329 <!-- test5 --> 329 <!-- test5 -->
330 <test> 330 <test expect_num_outputs="1">
331 <conditional name="prediction"> 331 <conditional name="prediction">
332 <param name="tool" value="processing"/> 332 <param name="tool" value="processing"/>
333 <param name="method" value="recommended"/> 333 <param name="method" value="recommended"/>
334 <conditional name="alleles"> 334 <conditional name="alleles">
335 <param name="allelesrc" value="entry"/> 335 <param name="allelesrc" value="entry"/>
346 <has_text text="LYNTVATLY" /> 346 <has_text text="LYNTVATLY" />
347 </assert_contents> 347 </assert_contents>
348 </output> 348 </output>
349 </test> 349 </test>
350 <!-- test6 --> 350 <!-- test6 -->
351 <test> 351 <test expect_num_outputs="1">
352 <conditional name="prediction"> 352 <conditional name="prediction">
353 <param name="tool" value="mhcnp"/> 353 <param name="tool" value="mhcnp"/>
354 <param name="method" value="mhcnp"/> 354 <param name="method" value="mhcnp"/>
355 <conditional name="alleles"> 355 <conditional name="alleles">
356 <param name="allelesrc" value="entry"/> 356 <param name="allelesrc" value="entry"/>
366 <has_text text="LYNTVATLY" /> 366 <has_text text="LYNTVATLY" />
367 </assert_contents> 367 </assert_contents>
368 </output> 368 </output>
369 </test> 369 </test>
370 <!-- test7 --> 370 <!-- test7 -->
371 <test> 371 <test expect_num_outputs="1">
372 <conditional name="prediction"> 372 <conditional name="prediction">
373 <param name="tool" value="bcell"/> 373 <param name="tool" value="bcell"/>
374 <param name="method" value="Emini"/> 374 <param name="method" value="Emini"/>
375 </conditional> 375 </conditional>
376 <conditional name="sequence"> 376 <conditional name="sequence">
382 <has_text text="VLSEGE" /> 382 <has_text text="VLSEGE" />
383 </assert_contents> 383 </assert_contents>
384 </output> 384 </output>
385 </test> 385 </test>
386 <!-- test8 --> 386 <!-- test8 -->
387 <test> 387 <test expect_num_outputs="1">
388 <conditional name="prediction"> 388 <conditional name="prediction">
389 <param name="tool" value="bcell"/> 389 <param name="tool" value="bcell"/>
390 <param name="method" value="Kolaskar-Tongaonkar"/> 390 <param name="method" value="Kolaskar-Tongaonkar"/>
391 <param name="window_size" value="9"/> 391 <param name="window_size" value="9"/>
392 </conditional> 392 </conditional>
395 <param name="seq_fasta" ftype="fasta" value="bcell.fa"/> 395 <param name="seq_fasta" ftype="fasta" value="bcell.fa"/>
396 </conditional> 396 </conditional>
397 <output name="output"> 397 <output name="output">
398 <assert_contents> 398 <assert_contents>
399 <has_text text="ADVAGH" /> 399 <has_text text="ADVAGH" />
400 </assert_contents>
401 </output>
402 </test>
403 <!-- test9 test 2nd output for Bepipred, no idea if its possible to have output non-empty -->
404 <test expect_num_outputs="2">
405 <conditional name="prediction">
406 <param name="tool" value="bcell"/>
407 <param name="method" value="Bepipred"/>
408 <param name="window_size" value="9"/>
409 </conditional>
410 <conditional name="sequence">
411 <param name="seqsrc" value="fasta"/>
412 <param name="seq_fasta" ftype="fasta" value="bcell.fa"/>
413 </conditional>
414 <output name="output">
415 <assert_contents>
416 <has_n_lines n="0" />
417 </assert_contents>
418 </output>
419 <output name="output2">
420 <assert_contents>
421 <has_n_lines n="106"/>
422 <has_n_columns n="5"/>
400 </assert_contents> 423 </assert_contents>
401 </output> 424 </output>
402 </test> 425 </test>
403 426
404 </tests> 427 </tests>