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comparison datasets_gene.xml @ 12:d78faac2c6ef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
author iuc
date Sat, 03 Dec 2022 13:29:32 +0000
parents ac24fff14f23
children 1e188c9610c3
comparison
equal deleted inserted replaced
11:ac24fff14f23 12:d78faac2c6ef
1 <tool id="datasets_download_gene" name="NCBI Datasets Gene" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="datasets_download_gene" name="NCBI Datasets Gene" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>download gene sequences and metadata</description> 2 <description>download gene sequences and metadata</description>
3 <expand macro="bio_tools"/>
3 <macros> 4 <macros>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
5 </macros> 6 </macros>
6 <expand macro="requirements"></expand> 7 <expand macro="requirements"></expand>
8 <expand macro="version_command"/>
7 <command><![CDATA[ 9 <command><![CDATA[
8 #import re 10 #import re
9 @SETUP_CERTIFICATES@ 11 @SETUP_CERTIFICATES@
10 datasets download gene $query.subcommand.download_by 12 datasets download gene $query.subcommand.download_by
11 #if $query.subcommand.download_by == 'taxon': 13 #if $query.subcommand.download_by == 'taxon':
284 </section> 286 </section>
285 <output name="gene_data_report"> 287 <output name="gene_data_report">
286 <assert_contents> 288 <assert_contents>
287 <has_text text="baboon"/> 289 <has_text text="baboon"/>
288 <has_text text="glyceraldehyde-3-phosphate dehydrogenase"/> 290 <has_text text="glyceraldehyde-3-phosphate dehydrogenase"/>
289 <has_n_lines n="31"/> 291 <has_n_lines min="30"/>
290 <has_n_columns n="8"/> 292 <has_n_columns n="8"/>
291 </assert_contents> 293 </assert_contents>
292 </output> 294 </output>
293 <output name="gene_fasta"> 295 <output name="gene_fasta">
294 <assert_contents> 296 <assert_contents>
348 </output> 350 </output>
349 <output name="gene_product_report"> 351 <output name="gene_product_report">
350 <assert_contents> 352 <assert_contents>
351 <has_text text="house mouse"/> 353 <has_text text="house mouse"/>
352 <has_text text="XR_004936704.1"/> 354 <has_text text="XR_004936704.1"/>
353 <has_n_lines n="137"/> 355 <has_n_lines min="130"/>
354 <has_n_columns n="38"/> 356 <has_n_columns n="38"/>
355 </assert_contents> 357 </assert_contents>
356 </output> 358 </output>
357 <output name="threep_utr_fasta"> 359 <output name="threep_utr_fasta">
358 <assert_contents> 360 <assert_contents>
382 </section> 384 </section>
383 <output name="gene_data_report"> 385 <output name="gene_data_report">
384 <assert_contents> 386 <assert_contents>
385 <has_text text="rat"/> 387 <has_text text="rat"/>
386 <has_text text="Brca1"/> 388 <has_text text="Brca1"/>
387 <has_n_lines n="38"/> 389 <has_n_lines min="30"/>
388 <has_n_columns n="8"/> 390 <has_n_columns n="8"/>
389 </assert_contents> 391 </assert_contents>
390 </output> 392 </output>
391 </test> 393 </test>
392 394
428 </conditional> 430 </conditional>
429 </section> 431 </section>
430 <output name="gene_data_report"> 432 <output name="gene_data_report">
431 <assert_contents> 433 <assert_contents>
432 <has_text text="human"/> 434 <has_text text="human"/>
433 <has_n_lines n="823"/> 435 <has_n_lines min="800"/>
434 <has_n_columns n="8"/> 436 <has_n_columns n="8"/>
435 </assert_contents> 437 </assert_contents>
436 </output> 438 </output>
437 </test> 439 </test>
438 440
486 </conditional> 488 </conditional>
487 </section> 489 </section>
488 <output name="gene_data_report"> 490 <output name="gene_data_report">
489 <assert_contents> 491 <assert_contents>
490 <has_text text="human"/> 492 <has_text text="human"/>
491 <has_n_lines n="72533"/> 493 <has_n_lines min="72000"/>
492 <has_n_columns n="8"/> 494 <has_n_columns n="8"/>
493 </assert_contents> 495 </assert_contents>
494 </output> 496 </output>
495 </test> 497 </test>
496 <!-- 11: datasets download gene taxon human + \-\-fasta-filter --> 498 <!-- 11: datasets download gene taxon human + \-\-fasta-filter -->
511 </conditional> 513 </conditional>
512 </section> 514 </section>
513 <output name="gene_data_report"> 515 <output name="gene_data_report">
514 <assert_contents> 516 <assert_contents>
515 <has_text text="human"/> 517 <has_text text="human"/>
516 <has_n_lines n="72533"/> 518 <has_n_lines min="72000"/>
517 <has_n_columns n="8"/> 519 <has_n_columns n="8"/>
518 </assert_contents> 520 </assert_contents>
519 </output> 521 </output>
520 <output name="protein_fasta"> 522 <output name="protein_fasta">
521 <assert_contents> 523 <assert_contents>