Mercurial > repos > galaxyp > eggnog_mapper
comparison eggnog_mapper.xml @ 11:5a30ae278db0 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
author | galaxyp |
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date | Mon, 20 Jun 2022 12:49:52 +0000 |
parents | bcb4895b8b55 |
children | 9d1fbff733cf |
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10:bcb4895b8b55 | 11:5a30ae278db0 |
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1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@+galaxy2"> | 1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
2 <description>functional sequence annotation by orthology</description> | 2 <description>functional sequence annotation by orthology</description> |
3 <macros> | 3 <macros> |
4 <import>eggnog_macros.xml</import> | 4 <import>eggnog_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
317 <action name="column_names" type="metadata" default="query,orth_type,species,orthologs"/> | 317 <action name="column_names" type="metadata" default="query,orth_type,species,orthologs"/> |
318 </actions> | 318 </actions> |
319 </data> | 319 </data> |
320 </outputs> | 320 </outputs> |
321 <tests> | 321 <tests> |
322 <test> | 322 <test expect_num_outputs="1"> |
323 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> | 323 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> |
324 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> | 324 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> |
325 <param name="no_annot" value="true"/> | 325 <param name="no_annot" value="true"/> |
326 <param name="no_file_comments" value="true"/> | 326 <param name="no_file_comments" value="true"/> |
327 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> | 327 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> |
328 <expand macro="stdout_assertion"/> | |
328 </test> | 329 </test> |
329 <test> | 330 <test expect_num_outputs="3"> |
330 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> | 331 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> |
331 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> | 332 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> |
332 <param name="report_orthologs" value="true"/> | 333 <param name="report_orthologs" value="true"/> |
333 <param name="no_file_comments" value="true"/> | 334 <param name="no_file_comments" value="true"/> |
334 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> | 335 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> |
335 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/> | 336 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/> |
336 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/> | 337 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/> |
338 <expand macro="stdout_assertion"/> | |
337 </test> | 339 </test> |
338 <test> | 340 <test expect_num_outputs="3"> |
339 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> | 341 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> |
340 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> | 342 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> |
341 <param name="report_orthologs" value="true"/> | 343 <param name="report_orthologs" value="true"/> |
342 <param name="no_file_comments" value="true"/> | 344 <param name="no_file_comments" value="true"/> |
343 <section name="annotation_options"> | 345 <section name="annotation_options"> |
344 <param name="tax_scope" value="651137" /> | 346 <param name="tax_scope" value="651137" /> |
345 </section> | 347 </section> |
346 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> | 348 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> |
347 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/> | 349 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/> |
348 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/> | 350 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/> |
351 <expand macro="stdout_assertion"/> | |
349 </test> | 352 </test> |
350 <test> | 353 <test expect_num_outputs="3"> |
351 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> | 354 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> |
352 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> | 355 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> |
353 <section name="seed_ortho_options"> | 356 <section name="seed_ortho_options"> |
354 <conditional name="ortho_method"> | 357 <conditional name="ortho_method"> |
355 <param name="m" value="diamond" /> | 358 <param name="m" value="diamond" /> |
359 <param name="report_orthologs" value="true"/> | 362 <param name="report_orthologs" value="true"/> |
360 <param name="no_file_comments" value="true"/> | 363 <param name="no_file_comments" value="true"/> |
361 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> | 364 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> |
362 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/> | 365 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/> |
363 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/> | 366 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/> |
367 <expand macro="stdout_assertion"/> | |
364 </test> | 368 </test> |
365 <!-- not enabled as it requires a specific .db file, hard to minimize --> | 369 <!-- not enabled as it requires a specific .db file, hard to minimize --> |
366 <!--test> | 370 <!--test> |
367 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> | 371 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> |
368 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> | 372 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> |