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comparison eggnog_mapper.xml @ 10:3d30526975d7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
author galaxyp
date Mon, 20 Jun 2022 12:48:22 +0000
parents bb2fd26a081d
children 1f2be4ae431f
comparison
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9:bb2fd26a081d 10:3d30526975d7
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@"/>