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comparison stringtie.xml @ 24:cbf488da3b2c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 8dc7b89b32a9e86c48e9ef7078703ae277bdaf96
author iuc
date Mon, 13 May 2024 14:07:55 +0000
parents 8eb8750070d4
children
comparison
equal deleted inserted replaced
23:8eb8750070d4 24:cbf488da3b2c
276 <test expect_num_outputs="1"> 276 <test expect_num_outputs="1">
277 <conditional name="input_options"> 277 <conditional name="input_options">
278 <param name="input_mode" value="short_reads"/> 278 <param name="input_mode" value="short_reads"/>
279 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> 279 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
280 </conditional> 280 </conditional>
281 <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" lines_diff="2"/> 281 <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" lines_diff="4"/>
282 </test> 282 </test>
283 <!--Ensure fraction option works --> 283 <!--Ensure fraction option works -->
284 <test expect_num_outputs="1"> 284 <test expect_num_outputs="1">
285 <conditional name="input_options"> 285 <conditional name="input_options">
286 <param name="input_mode" value="short_reads"/> 286 <param name="input_mode" value="short_reads"/>
287 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> 287 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
288 </conditional> 288 </conditional>
289 <param name="fraction" value="0.17"/> 289 <param name="fraction" value="0.17"/>
290 <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" lines_diff="2"/> 290 <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" lines_diff="4"/>
291 </test> 291 </test>
292 <!--Ensure guide option works --> 292 <!--Ensure guide option works -->
293 <test expect_num_outputs="1"> 293 <test expect_num_outputs="1">
294 <conditional name="input_options"> 294 <conditional name="input_options">
295 <param name="input_mode" value="short_reads"/> 295 <param name="input_mode" value="short_reads"/>
296 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> 296 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
297 </conditional> 297 </conditional>
298 <param name="use_guide" value="yes"/> 298 <param name="use_guide" value="yes"/>
299 <param name="guide_gff_select" value="history"/> 299 <param name="guide_gff_select" value="history"/>
300 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> 300 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
301 <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" lines_diff="2"/> 301 <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" lines_diff="4"/>
302 </test> 302 </test>
303 <!--Ensure guide with fraction works --> 303 <!--Ensure guide with fraction works -->
304 <test expect_num_outputs="1"> 304 <test expect_num_outputs="1">
305 <conditional name="input_options"> 305 <conditional name="input_options">
306 <param name="input_mode" value="short_reads"/> 306 <param name="input_mode" value="short_reads"/>
308 </conditional> 308 </conditional>
309 <param name="use_guide" value="yes"/> 309 <param name="use_guide" value="yes"/>
310 <param name="guide_gff_select" value="history"/> 310 <param name="guide_gff_select" value="history"/>
311 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/> 311 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/>
312 <param name="fraction" value="0.17"/> 312 <param name="fraction" value="0.17"/>
313 <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="2"/> 313 <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="4"/>
314 </test> 314 </test>
315 <!--Ensure coverage and output for Ballgown works --> 315 <!--Ensure coverage and output for Ballgown works -->
316 <test expect_num_outputs="7"> 316 <test expect_num_outputs="7">
317 <conditional name="input_options"> 317 <conditional name="input_options">
318 <param name="input_mode" value="short_reads"/> 318 <param name="input_mode" value="short_reads"/>
326 <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular"/> 326 <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular"/>
327 <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular"/> 327 <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular"/>
328 <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular"/> 328 <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular"/>
329 <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular"/> 329 <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular"/>
330 <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular"/> 330 <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular"/>
331 <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="2"/> 331 <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="4"/>
332 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="2"/> 332 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="4"/>
333 </test> 333 </test>
334 <!--Ensure output for edgeR works --> 334 <!--Ensure output for edgeR works -->
335 <test expect_num_outputs="5"> 335 <test expect_num_outputs="5">
336 <conditional name="input_options"> 336 <conditional name="input_options">
337 <param name="input_mode" value="short_reads"/> 337 <param name="input_mode" value="short_reads"/>
345 <param name="coverage_file" value="true"/> 345 <param name="coverage_file" value="true"/>
346 <param name="clustering" value="true"/> 346 <param name="clustering" value="true"/>
347 <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular"/> 347 <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular"/>
348 <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular"/> 348 <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular"/>
349 <output name="legend" file="legend.tsv" ftype="tabular"/> 349 <output name="legend" file="legend.tsv" ftype="tabular"/>
350 <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="2"/> 350 <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="4"/>
351 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="2"/> 351 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="4"/>
352 </test> 352 </test>
353 <!--Ensure gene abundances output works --> 353 <!--Ensure gene abundances output works -->
354 <test expect_num_outputs="2"> 354 <test expect_num_outputs="2">
355 <conditional name="input_options"> 355 <conditional name="input_options">
356 <param name="input_mode" value="short_reads"/> 356 <param name="input_mode" value="short_reads"/>
359 <param name="use_guide" value="yes"/> 359 <param name="use_guide" value="yes"/>
360 <param name="guide_gff_select" value="history"/> 360 <param name="guide_gff_select" value="history"/>
361 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/> 361 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/>
362 <param name="fraction" value="0.17"/> 362 <param name="fraction" value="0.17"/>
363 <param name="abundance_estimation" value="true"/> 363 <param name="abundance_estimation" value="true"/>
364 <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="2"/> 364 <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="4"/>
365 <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" /> 365 <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="4" />
366 </test> 366 </test>
367 <!--Ensure another fraction value works --> 367 <!--Ensure another fraction value works -->
368 <test expect_num_outputs="1"> 368 <test expect_num_outputs="1">
369 <conditional name="input_options"> 369 <conditional name="input_options">
370 <param name="input_mode" value="short_reads"/> 370 <param name="input_mode" value="short_reads"/>
372 </conditional> 372 </conditional>
373 <param name="use_guide" value="yes"/> 373 <param name="use_guide" value="yes"/>
374 <param name="guide_gff_select" value="history"/> 374 <param name="guide_gff_select" value="history"/>
375 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/> 375 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/>
376 <param name="fraction" value="0.15"/> 376 <param name="fraction" value="0.15"/>
377 <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="2"/> 377 <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="4"/>
378 </test> 378 </test>
379 <!--Ensure built-in GTFs work --> 379 <!--Ensure built-in GTFs work -->
380 <test expect_num_outputs="1"> 380 <test expect_num_outputs="1">
381 <conditional name="input_options"> 381 <conditional name="input_options">
382 <param name="input_mode" value="short_reads"/> 382 <param name="input_mode" value="short_reads"/>
383 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> 383 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
384 </conditional> 384 </conditional>
385 <param name="use_guide" value="yes"/> 385 <param name="use_guide" value="yes"/>
386 <param name="guide_gff_select" value="cached"/> 386 <param name="guide_gff_select" value="cached"/>
387 <param name="fraction" value="0.15"/> 387 <param name="fraction" value="0.15"/>
388 <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="2"/> 388 <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="4"/>
389 </test> 389 </test>
390 <!-- Test long reads input --> 390 <!-- Test long reads input -->
391 <test expect_num_outputs="1"> 391 <test expect_num_outputs="1">
392 <conditional name="input_options"> 392 <conditional name="input_options">
393 <param name="input_mode" value="long_reads"/> 393 <param name="input_mode" value="long_reads"/>
394 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> 394 <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
395 </conditional> 395 </conditional>
396 <param name="use_guide" value="yes"/> 396 <param name="use_guide" value="yes"/>
397 <param name="guide_gff_select" value="cached"/> 397 <param name="guide_gff_select" value="cached"/>
398 <param name="fraction" value="0.15"/> 398 <param name="fraction" value="0.15"/>
399 <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="2"/> 399 <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="4"/>
400 </test> 400 </test>
401 <!-- Test error splice option --> 401 <!-- Test error splice option -->
402 <test expect_num_outputs="1"> 402 <test expect_num_outputs="1">
403 <conditional name="input_options"> 403 <conditional name="input_options">
404 <param name="input_mode" value="long_reads"/> 404 <param name="input_mode" value="long_reads"/>
406 <param name="error_splice" value="30"/> 406 <param name="error_splice" value="30"/>
407 </conditional> 407 </conditional>
408 <param name="use_guide" value="yes"/> 408 <param name="use_guide" value="yes"/>
409 <param name="guide_gff_select" value="cached"/> 409 <param name="guide_gff_select" value="cached"/>
410 <param name="fraction" value="0.15"/> 410 <param name="fraction" value="0.15"/>
411 <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="2"/> 411 <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="4"/>
412 </test> 412 </test>
413 <!-- Test mixed reads input --> 413 <!-- Test mixed reads input -->
414 <test expect_num_outputs="1"> 414 <test expect_num_outputs="1">
415 <conditional name="input_options"> 415 <conditional name="input_options">
416 <param name="input_mode" value="mixed_reads"/> 416 <param name="input_mode" value="mixed_reads"/>