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comparison stringtie.xml @ 26:d8424a4f39ed draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb
author iuc
date Wed, 27 Jul 2022 09:27:31 +0000
parents 93404dcc9c96
children 95d141564e5d
comparison
equal deleted inserted replaced
25:93404dcc9c96 26:d8424a4f39ed
275 <test expect_num_outputs="1"> 275 <test expect_num_outputs="1">
276 <conditional name="input_options"> 276 <conditional name="input_options">
277 <param name="input_mode" value="short_reads"/> 277 <param name="input_mode" value="short_reads"/>
278 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> 278 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
279 </conditional> 279 </conditional>
280 <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" lines_diff="4" /> 280 <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
281 </test> 281 </test>
282 <!--Ensure fraction option works --> 282 <!--Ensure fraction option works -->
283 <test expect_num_outputs="1"> 283 <test expect_num_outputs="1">
284 <conditional name="input_options"> 284 <conditional name="input_options">
285 <param name="input_mode" value="short_reads"/> 285 <param name="input_mode" value="short_reads"/>
286 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> 286 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
287 </conditional> 287 </conditional>
288 <param name="fraction" value="0.17" /> 288 <param name="fraction" value="0.17" />
289 <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" lines_diff="4" /> 289 <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
290 </test> 290 </test>
291 <!--Ensure guide option works --> 291 <!--Ensure guide option works -->
292 <test expect_num_outputs="1"> 292 <test expect_num_outputs="1">
293 <conditional name="input_options"> 293 <conditional name="input_options">
294 <param name="input_mode" value="short_reads"/> 294 <param name="input_mode" value="short_reads"/>
295 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> 295 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
296 </conditional> 296 </conditional>
297 <param name="use_guide" value="yes" /> 297 <param name="use_guide" value="yes" />
298 <param name="guide_gff_select" value="history" /> 298 <param name="guide_gff_select" value="history" />
299 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> 299 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
300 <output name="output_gtf" file="stringtie_out3.gtf" ftype="gtf" lines_diff="4" /> 300 <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
301 </test> 301 </test>
302 <!--Ensure guide with fraction works --> 302 <!--Ensure guide with fraction works -->
303 <test expect_num_outputs="1"> 303 <test expect_num_outputs="1">
304 <conditional name="input_options"> 304 <conditional name="input_options">
305 <param name="input_mode" value="short_reads"/> 305 <param name="input_mode" value="short_reads"/>
307 </conditional> 307 </conditional>
308 <param name="use_guide" value="yes" /> 308 <param name="use_guide" value="yes" />
309 <param name="guide_gff_select" value="history" /> 309 <param name="guide_gff_select" value="history" />
310 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> 310 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
311 <param name="fraction" value="0.17" /> 311 <param name="fraction" value="0.17" />
312 <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" /> 312 <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
313 </test> 313 </test>
314 <!--Ensure coverage and output for Ballgown works --> 314 <!--Ensure coverage and output for Ballgown works -->
315 <test expect_num_outputs="7"> 315 <test expect_num_outputs="7">
316 <conditional name="input_options"> 316 <conditional name="input_options">
317 <param name="input_mode" value="short_reads"/> 317 <param name="input_mode" value="short_reads"/>
325 <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" /> 325 <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" />
326 <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" /> 326 <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" />
327 <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" /> 327 <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" />
328 <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" /> 328 <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" />
329 <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" /> 329 <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" />
330 <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="4" /> 330 <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" compare="re_match" sort="true"/>
331 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" /> 331 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
332 </test> 332 </test>
333 <!--Ensure output for edgeR works --> 333 <!--Ensure output for edgeR works -->
334 <test expect_num_outputs="5"> 334 <test expect_num_outputs="5">
335 <conditional name="input_options"> 335 <conditional name="input_options">
336 <param name="input_mode" value="short_reads"/> 336 <param name="input_mode" value="short_reads"/>
344 <param name="coverage_file" value="true" /> 344 <param name="coverage_file" value="true" />
345 <param name="clustering" value="true" /> 345 <param name="clustering" value="true" />
346 <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" /> 346 <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" />
347 <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" /> 347 <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" />
348 <output name="legend" file="legend.tsv" ftype="tabular" /> 348 <output name="legend" file="legend.tsv" ftype="tabular" />
349 <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="4" /> 349 <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" compare="re_match" sort="true"/>
350 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" /> 350 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
351 </test> 351 </test>
352 <!--Ensure gene abundances output works --> 352 <!--Ensure gene abundances output works -->
353 <test expect_num_outputs="2"> 353 <test expect_num_outputs="2">
354 <conditional name="input_options"> 354 <conditional name="input_options">
355 <param name="input_mode" value="short_reads"/> 355 <param name="input_mode" value="short_reads"/>
358 <param name="use_guide" value="yes" /> 358 <param name="use_guide" value="yes" />
359 <param name="guide_gff_select" value="history" /> 359 <param name="guide_gff_select" value="history" />
360 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> 360 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
361 <param name="fraction" value="0.17" /> 361 <param name="fraction" value="0.17" />
362 <param name="abundance_estimation" value="true" /> 362 <param name="abundance_estimation" value="true" />
363 <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" /> 363 <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
364 <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" /> 364 <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" />
365 </test> 365 </test>
366 <!--Ensure another fraction value works --> 366 <!--Ensure another fraction value works -->
367 <test expect_num_outputs="1"> 367 <test expect_num_outputs="1">
368 <conditional name="input_options"> 368 <conditional name="input_options">
371 </conditional> 371 </conditional>
372 <param name="use_guide" value="yes" /> 372 <param name="use_guide" value="yes" />
373 <param name="guide_gff_select" value="history" /> 373 <param name="guide_gff_select" value="history" />
374 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> 374 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
375 <param name="fraction" value="0.15" /> 375 <param name="fraction" value="0.15" />
376 <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="4" /> 376 <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" compare="re_match" sort="true"/>
377 </test> 377 </test>
378 <!--Ensure built-in GTFs work --> 378 <!--Ensure built-in GTFs work -->
379 <test expect_num_outputs="1"> 379 <test expect_num_outputs="1">
380 <conditional name="input_options"> 380 <conditional name="input_options">
381 <param name="input_mode" value="short_reads"/> 381 <param name="input_mode" value="short_reads"/>
382 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> 382 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
383 </conditional> 383 </conditional>
384 <param name="use_guide" value="yes" /> 384 <param name="use_guide" value="yes" />
385 <param name="guide_gff_select" value="cached" /> 385 <param name="guide_gff_select" value="cached" />
386 <param name="fraction" value="0.15" /> 386 <param name="fraction" value="0.15" />
387 <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="4" /> 387 <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" compare="re_match" sort="true"/>
388 </test> 388 </test>
389 <!-- Test long reads input --> 389 <!-- Test long reads input -->
390 <test expect_num_outputs="1"> 390 <test expect_num_outputs="1">
391 <conditional name="input_options"> 391 <conditional name="input_options">
392 <param name="input_mode" value="long_reads"/> 392 <param name="input_mode" value="long_reads"/>
393 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> 393 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
394 </conditional> 394 </conditional>
395 <param name="use_guide" value="yes" /> 395 <param name="use_guide" value="yes" />
396 <param name="guide_gff_select" value="cached" /> 396 <param name="guide_gff_select" value="cached" />
397 <param name="fraction" value="0.15" /> 397 <param name="fraction" value="0.15" />
398 <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="4" /> 398 <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" compare="re_match" sort="true"/>
399 </test> 399 </test>
400 <!-- Test error splice option --> 400 <!-- Test error splice option -->
401 <test expect_num_outputs="1"> 401 <test expect_num_outputs="1">
402 <conditional name="input_options"> 402 <conditional name="input_options">
403 <param name="input_mode" value="long_reads"/> 403 <param name="input_mode" value="long_reads"/>
405 <param name="error_splice" value="30" /> 405 <param name="error_splice" value="30" />
406 </conditional> 406 </conditional>
407 <param name="use_guide" value="yes" /> 407 <param name="use_guide" value="yes" />
408 <param name="guide_gff_select" value="cached" /> 408 <param name="guide_gff_select" value="cached" />
409 <param name="fraction" value="0.15" /> 409 <param name="fraction" value="0.15" />
410 <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="4" /> 410 <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" compare="re_match" sort="true"/>
411 </test> 411 </test>
412 <!-- Test mixed reads input --> 412 <!-- Test mixed reads input -->
413 <test expect_num_outputs="1"> 413 <test expect_num_outputs="1">
414 <conditional name="input_options"> 414 <conditional name="input_options">
415 <param name="input_mode" value="mixed_reads"/> 415 <param name="input_mode" value="mixed_reads"/>
416 <param name="input_bam_short" ftype="bam" value="short_reads.bam" /> 416 <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
417 <param name="input_bam_long" ftype="bam" value="long_reads.bam" /> 417 <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
418 </conditional> 418 </conditional>
419 <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" lines_diff="4" /> 419 <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
420 </test> 420 </test>
421 </tests> 421 </tests>
422 <help><![CDATA[ 422 <help><![CDATA[
423 423
424 .. class:: infomark 424 .. class:: infomark