Mercurial > repos > artbio > rsem
comparison rsem-bwt2.xml @ 5:835a2f3372b5 draft
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8
author | artbio |
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date | Sat, 02 Jun 2018 06:10:54 -0400 |
parents | 1823c8e07d96 |
children | 45a30e216fec |
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4:1823c8e07d96 | 5:835a2f3372b5 |
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161 <option value="index">Build rsem reference</option> | 161 <option value="index">Build rsem reference</option> |
162 <option value="no-index" selected="true">rsem reference available from history</option> | 162 <option value="no-index" selected="true">rsem reference available from history</option> |
163 </param> | 163 </param> |
164 <when value="index"> | 164 <when value="index"> |
165 <conditional name="self_reference"> | 165 <conditional name="self_reference"> |
166 <param name="ref_type" type="select" label="Reference transcript source"> | 166 <param name="ref_type" type="select" label="Reference source"> |
167 <option value="transcripts">transcript fasta</option> | 167 <option value="transcripts">transcript fasta</option> |
168 <option value="genomic">reference genome and gtf</option> | 168 <option value="genomic">reference genome and gtf</option> |
169 </param> | 169 </param> |
170 <when value="transcripts"> | 170 <when value="transcripts"> |
171 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" | 171 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" |
226 <when value="Yes"> | 226 <when value="Yes"> |
227 <param name="sample" type="text" value="rsem_sample" label="Sample name" /> | 227 <param name="sample" type="text" value="rsem_sample" label="Sample name" /> |
228 <conditional name="reference"> | 228 <conditional name="reference"> |
229 <param name="refSrc" type="select" label="RSEM Reference Source"> | 229 <param name="refSrc" type="select" label="RSEM Reference Source"> |
230 <option value="history">From your history</option> | 230 <option value="history">From your history</option> |
231 <option value="self">Prepare RSEM Reference with this tool</option> | 231 <option value="self">RSEM Reference prepared with this tool</option> |
232 </param> | 232 </param> |
233 <when value="history"> | 233 <when value="history"> |
234 <param name="rsem_ref" type="data" format="rsem_bt2_ref" label="RSEM reference" /> | 234 <param name="rsem_ref" type="data" format="rsem_bt2_ref" label="RSEM reference" /> |
235 </when> | 235 </when> |
236 <when value="self"> | 236 <when value="self"> |
324 | 324 |
325 <tests> | 325 <tests> |
326 <test> | 326 <test> |
327 <param name="select_job" value="index"/> | 327 <param name="select_job" value="index"/> |
328 <param name="ref_type" value="genomic"/> | 328 <param name="ref_type" value="genomic"/> |
329 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> | 329 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/> |
330 <param name="gtf" value="ref.gtf" ftype="gtf"/> | 330 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/> |
331 <param name="reference_name" value="ref"/> | 331 <param name="reference_name" value="ebola_genome"/> |
332 <param name="select" value="Yes"/> | 332 <param name="select" value="Yes"/> |
333 <param name="sample" value="rsem_sample"/> | 333 <param name="sample" value="ebola_RNAseq"/> |
334 <param name="refSrc" value="self"/> | 334 <param name="refSrc" value="self"/> |
335 <param name="format" value="fastq"/> | 335 <param name="format" value="fastq"/> |
336 <param name="matepair" value="single"/> | 336 <param name="matepair" value="single"/> |
337 <param name="singlefastq" value="test.fq" ftype="fastqsanger"/> | 337 <param name="singlefastq" value="Ebola_forward.fastqsanger" ftype="fastqsanger"/> |
338 <param name="result_bams" value="none"/> | 338 <param name="result_bams" value="none"/> |
339 <output name="reference_file"> | 339 <output name="reference_file"> |
340 <assert_contents> | 340 <assert_contents> |
341 <has_text text="ref" /> | 341 <has_text text="ebola_genome" /> |
342 </assert_contents> | 342 </assert_contents> |
343 </output> | 343 </output> |
344 <output name="gene_abundances" value="gene_abundances.tab2"/> | 344 <output name="gene_abundances" value="refgen_gene_abundances.bt2.tab"/> |
345 <output name="isoform_abundances" value="isoform_abundances.tab2" /> | 345 <output name="isoform_abundances" value="refgen_isoform_abundances.bt2.tab" /> |
346 <output name="log"> | 346 <output name="log"> |
347 <assert_contents> | 347 <assert_contents> |
348 <has_text text="Expression Results are written" /> | 348 <has_text text="Expression Results are written" /> |
349 </assert_contents> | 349 </assert_contents> |
350 </output> | 350 </output> |
351 </test> | 351 </test> |
352 <!-- ungzipped paired-end fastqsanger --> | |
353 <test> | 352 <test> |
353 <!-- test paired end on ebola genome --> | |
354 <param name="select_job" value="index"/> | 354 <param name="select_job" value="index"/> |
355 <param name="ref_type" value="genomic"/> | 355 <param name="ref_type" value="genomic"/> |
356 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> | 356 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/> |
357 <param name="gtf" value="ref.gtf" ftype="gtf"/> | 357 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/> |
358 <param name="reference_name" value="ref"/> | 358 <param name="reference_name" value="ebola"/> |
359 <param name="select" value="Yes"/> | |
360 <param name="sample" value="ebola_RNAseq"/> | |
361 <param name="refSrc" value="self"/> | |
362 <param name="format" value="fastq"/> | |
363 <param name="matepair" value="paired"/> | |
364 <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger.gz"/> | |
365 <param name="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/> | |
366 <param name="result_bams" value="both"/> | |
367 <output name="reference_file"> | |
368 <assert_contents> | |
369 <has_text text="ebola" /> | |
370 </assert_contents> | |
371 </output> | |
372 <output name="gene_abundances" value="paired_refgen_gene_abundances.bt2.tab"/> | |
373 <output name="isoform_abundances" value="paired_refgen_isoform_abundances.bt2.tab" /> | |
374 <output name="transcript_sorted_bam" value="paired_refgen_transcripts.bt2.bam" ftype="bam" lines_diff="2" /> | |
375 <output name="genome_sorted_bam" value="paired_refgen_isoform_abundances.bt2.bam" ftype="bam" lines_diff="2" /> | |
376 <output name="log"> | |
377 <assert_contents> | |
378 <has_text text="Expression Results are written" /> | |
379 </assert_contents> | |
380 </output> | |
381 </test> | |
382 <test> | |
383 <!-- test paired end on ebola transcripts --> | |
384 <param name="select_job" value="index"/> | |
385 <param name="ref_type" value="transcripts"/> | |
386 <param name="reference_fasta_file" value="Ebola_transcripts.fa" ftype="fasta"/> | |
387 <param name="transcript_to_gene_map" value="ebola_gene_transcript_table.txt" ftype="gtf"/> | |
388 <param name="reference_name" value="ebola"/> | |
389 <param name="select" value="Yes"/> | |
390 <param name="sample" value="ebola_RNAseq"/> | |
391 <param name="refSrc" value="self"/> | |
392 <param name="format" value="fastq"/> | |
393 <param name="matepair" value="paired"/> | |
394 <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger.gz"/> | |
395 <param name="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/> | |
396 <param name="result_bams" value="default"/> | |
397 <output name="reference_file"> | |
398 <assert_contents> | |
399 <has_text text="ebola" /> | |
400 </assert_contents> | |
401 </output> | |
402 <output name="gene_abundances" value="paired_reftrans_gene_abundances.bt2.tab"/> | |
403 <output name="isoform_abundances" value="paired_reftrans_isoform_abundances.bt2.tab" /> | |
404 <output name="transcript_sorted_bam" value="paired_reftrans_transcripts.bt2.bam" ftype="bam" lines_diff="2" /> | |
405 <output name="log"> | |
406 <assert_contents> | |
407 <has_text text="Expression Results are written" /> | |
408 </assert_contents> | |
409 </output> | |
410 </test> | |
411 <test> | |
412 <param name="select_job" value="index"/> | |
413 <param name="ref_type" value="genomic"/> | |
414 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/> | |
415 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/> | |
416 <param name="reference_name" value="ebola"/> | |
359 <param name="select" value="Yes"/> | 417 <param name="select" value="Yes"/> |
360 <param name="sample" value="rsem_sample"/> | 418 <param name="sample" value="rsem_sample"/> |
361 <param name="refSrc" value="self"/> | 419 <param name="refSrc" value="self"/> |
362 <param name="format" value="fastq"/> | 420 <param name="format" value="fastq"/> |
363 <param name="matepair" value="single"/> | 421 <param name="matepair" value="single"/> |
364 <param name="singlefastq" value="test.fastq.gz" ftype="fastqsanger.gz"/> | 422 <param name="singlefastq" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/> |
365 <param name="result_bams" value="none"/> | 423 <param name="result_bams" value="none"/> |
366 <output name="reference_file"> | 424 <output name="reference_file"> |
367 <assert_contents> | 425 <assert_contents> |
368 <has_text text="ref" /> | 426 <has_text text="ebola" /> |
369 </assert_contents> | 427 </assert_contents> |
370 </output> | 428 </output> |
371 <output name="gene_abundances" value="gene_abundances.tab2"/> | 429 <output name="gene_abundances" value="single_refgen_gene_abundances.bt2.tab"/> |
372 <output name="isoform_abundances" value="isoform_abundances.tab2" /> | 430 <output name="isoform_abundances" value="single_refgen_isoform_abundances.bt2.tab" /> |
373 <output name="log"> | 431 <output name="log"> |
374 <assert_contents> | 432 <assert_contents> |
375 <has_text text="Expression Results are written" /> | 433 <has_text text="Expression Results are written" /> |
376 </assert_contents> | 434 </assert_contents> |
377 </output> | 435 </output> |
378 </test> | 436 </test> |
379 <test> | 437 <test> |
380 <param name="select_job" value="index"/> | 438 <param name="select_job" value="index"/> |
381 <param name="ref_type" value="genomic"/> | 439 <param name="ref_type" value="genomic"/> |
382 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> | 440 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/> |
383 <param name="gtf" value="ref.gtf" ftype="gtf"/> | 441 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/> |
384 <param name="reference_name" value="ref"/> | 442 <param name="reference_name" value="alone"/> |
385 <param name="select" value="No"/> | 443 <param name="select" value="No"/> |
386 <output name="reference_file"> | 444 <output name="reference_file"> |
387 <assert_contents> | 445 <assert_contents> |
388 <has_text text="ref" /> | 446 <has_text text="alone" /> |
389 </assert_contents> | 447 </assert_contents> |
390 </output> | 448 </output> |
391 </test> | 449 </test> |
392 </tests> | 450 </tests> |
393 | 451 |