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comparison rsem.xml @ 5:835a2f3372b5 draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8
author artbio
date Sat, 02 Jun 2018 06:10:54 -0400
parents 1823c8e07d96
children 45a30e216fec
comparison
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4:1823c8e07d96 5:835a2f3372b5
168 <option value="index">Build rsem reference</option> 168 <option value="index">Build rsem reference</option>
169 <option value="no-index" selected="true">rsem reference available from history</option> 169 <option value="no-index" selected="true">rsem reference available from history</option>
170 </param> 170 </param>
171 <when value="index"> 171 <when value="index">
172 <conditional name="self_reference"> 172 <conditional name="self_reference">
173 <param name="ref_type" type="select" label="Reference transcript source"> 173 <param name="ref_type" type="select" label="Reference source">
174 <option value="transcripts">transcript fasta</option> 174 <option value="transcripts">transcript fasta</option>
175 <option value="genomic">reference genome and gtf</option> 175 <option value="genomic">reference genome and gtf</option>
176 </param> 176 </param>
177 <when value="transcripts"> 177 <when value="transcripts">
178 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" 178 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
233 <when value="Yes"> 233 <when value="Yes">
234 <param name="sample" type="text" value="rsem_sample" label="Sample name" /> 234 <param name="sample" type="text" value="rsem_sample" label="Sample name" />
235 <conditional name="reference"> 235 <conditional name="reference">
236 <param name="refSrc" type="select" label="RSEM Reference Source"> 236 <param name="refSrc" type="select" label="RSEM Reference Source">
237 <option value="history">From your history</option> 237 <option value="history">From your history</option>
238 <option value="self">Prepare RSEM Reference with this tool</option> 238 <option value="self">RSEM Reference prepared with this tool</option>
239 </param> 239 </param>
240 <when value="history"> 240 <when value="history">
241 <param name="rsem_ref" type="data" format="rsem_ref" label="RSEM reference" /> 241 <param name="rsem_ref" type="data" format="rsem_ref" label="RSEM reference" />
242 </when> 242 </when>
243 <when value="self"> 243 <when value="self">
331 331
332 <tests> 332 <tests>
333 <test> 333 <test>
334 <param name="select_job" value="index"/> 334 <param name="select_job" value="index"/>
335 <param name="ref_type" value="genomic"/> 335 <param name="ref_type" value="genomic"/>
336 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> 336 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
337 <param name="gtf" value="ref.gtf" ftype="gtf"/> 337 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
338 <param name="reference_name" value="ref"/> 338 <param name="reference_name" value="ebola"/>
339 <param name="select" value="Yes"/> 339 <param name="select" value="Yes"/>
340 <param name="sample" value="rsem_sample"/> 340 <param name="sample" value="ebola_RNAseq"/>
341 <param name="refSrc" value="self"/> 341 <param name="refSrc" value="self"/>
342 <param name="format" value="fastq"/> 342 <param name="format" value="fastq"/>
343 <param name="matepair" value="single"/> 343 <param name="matepair" value="single"/>
344 <param name="singlefastq" value="test.fq" ftype="fastqsanger"/> 344 <param name="singlefastq" value="Ebola_forward.fastqsanger" ftype="fastqsanger"/>
345 <param name="result_bams" value="none"/> 345 <param name="result_bams" value="none"/>
346 <output name="reference_file"> 346 <output name="reference_file">
347 <assert_contents> 347 <assert_contents>
348 <has_text text="ref" /> 348 <has_text text="ebola" />
349 </assert_contents> 349 </assert_contents>
350 </output> 350 </output>
351 <output name="gene_abundances" value="gene_abundances.tab"/> 351 <output name="gene_abundances" value="refgen_gene_abundances.bt.tab"/>
352 <output name="isoform_abundances" value="isoform_abundances.tab" /> 352 <output name="isoform_abundances" value="refgen_isoform_abundances.bt.tab" />
353 <output name="log"> 353 <output name="log">
354 <assert_contents> 354 <assert_contents>
355 <has_text text="Expression Results are written" /> 355 <has_text text="Expression Results are written" />
356 </assert_contents> 356 </assert_contents>
357 </output> 357 </output>
358 </test> 358 </test>
359 <test> 359 <test>
360 <!-- test fastqsanger paired end --> 360 <!-- test fastqsanger paired end Ebola genome-->
361 <param name="select_job" value="index"/> 361 <param name="select_job" value="index"/>
362 <param name="ref_type" value="genomic"/> 362 <param name="ref_type" value="genomic"/>
363 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> 363 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
364 <param name="gtf" value="ref.gtf" ftype="gtf"/> 364 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
365 <param name="reference_name" value="ref"/> 365 <param name="reference_name" value="ebola"/>
366 <param name="select" value="Yes"/> 366 <param name="select" value="Yes"/>
367 <param name="sample" value="rsem_sample"/> 367 <param name="sample" value="rsem_sample"/>
368 <param name="refSrc" value="self"/> 368 <param name="refSrc" value="self"/>
369 <param name="format" value="fastq"/> 369 <param name="format" value="fastq"/>
370 <param name="matepair" value="paired"/> 370 <param name="matepair" value="paired"/>
371 <param name="fastq1" value="test2_forward.fastq" ftype="fastqsanger"/> 371 <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger"/>
372 <param name="fastq2" value="test2_reverse.fastq" ftype="fastqsanger"/> 372 <param name="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger"/>
373 <param name="result_bams" value="none" /> 373 <param name="result_bams" value="both" />
374 <output name="reference_file"> 374 <output name="reference_file">
375 <assert_contents> 375 <assert_contents>
376 <has_text text="ref" /> 376 <has_text text="ebola" />
377 </assert_contents> 377 </assert_contents>
378 </output> 378 </output>
379 <output name="gene_abundances" value="de_gene_abundances.tab"/> 379 <output name="gene_abundances" value="paired_refgen_gene_abundances.bt.tab"/>
380 <output name="isoform_abundances" value="de_isoform_abundances.tab" /> 380 <output name="isoform_abundances" value="paired_refgen_isoform_abundances.bt.tab" />
381 <output name="transcript_sorted_bam" value="paired_refgen_transcripts.bt.bam" ftype="bam" lines_diff="2" />
382 <output name="genome_sorted_bam" value="paired_refgen_isoform_abundances.bt.bam" ftype="bam" lines_diff="2" />
383 <output name="log">
384 <assert_contents>
385 <has_text text="Expression Results are written" />
386 </assert_contents>
387 </output>
388 </test>
389 <test>
390 <!-- test fastqsanger paired end Ebola transcripts -->
391 <param name="select_job" value="index"/>
392 <param name="ref_type" value="transcripts"/>
393 <param name="reference_fasta_file" value="Ebola_transcripts.fa" ftype="fasta"/>
394 <param name="transcript_to_gene_map" value="ebola_gene_transcript_table.txt" ftype="tabular"/>
395 <param name="reference_name" value="ebola"/>
396 <param name="select" value="Yes"/>
397 <param name="sample" value="rsem_sample"/>
398 <param name="refSrc" value="self"/>
399 <param name="format" value="fastq"/>
400 <param name="matepair" value="paired"/>
401 <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger"/>
402 <param name="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger"/>
403 <param name="result_bams" value="default" />
404 <output name="reference_file">
405 <assert_contents>
406 <has_text text="ebola" />
407 </assert_contents>
408 </output>
409 <output name="gene_abundances" value="paired_reftrans_gene_abundances.bt.tab"/>
410 <output name="isoform_abundances" value="paired_reftrans_isoform_abundances.bt.tab" />
411 <output name="transcript_sorted_bam" value="paired_reftrans_transcripts.bt.bam" ftype="bam" lines_diff="2" />
381 <output name="log"> 412 <output name="log">
382 <assert_contents> 413 <assert_contents>
383 <has_text text="Expression Results are written" /> 414 <has_text text="Expression Results are written" />
384 </assert_contents> 415 </assert_contents>
385 </output> 416 </output>
386 </test> 417 </test>
387 <test> 418 <test>
388 <param name="select_job" value="index"/> 419 <param name="select_job" value="index"/>
389 <param name="ref_type" value="genomic"/> 420 <param name="ref_type" value="genomic"/>
390 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> 421 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
391 <param name="gtf" value="ref.gtf" ftype="gtf"/> 422 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
392 <param name="reference_name" value="ref"/> 423 <param name="reference_name" value="ebola"/>
393 <param name="select" value="Yes"/> 424 <param name="select" value="Yes"/>
394 <param name="sample" value="rsem_sample"/> 425 <param name="sample" value="rsem_sample"/>
395 <param name="refSrc" value="self"/> 426 <param name="refSrc" value="self"/>
396 <param name="format" value="fastq"/> 427 <param name="format" value="fastq"/>
397 <param name="matepair" value="single"/> 428 <param name="matepair" value="single"/>
398 <param name="singlefastq" value="test.fastq.gz" ftype="fastqsanger.gz"/> 429 <param name="singlefastq" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
399 <param name="result_bams" value="none"/> 430 <param name="result_bams" value="none"/>
400 <output name="reference_file"> 431 <output name="reference_file">
401 <assert_contents> 432 <assert_contents>
402 <has_text text="ref" /> 433 <has_text text="ebola" />
403 </assert_contents> 434 </assert_contents>
404 </output> 435 </output>
405 <output name="gene_abundances" value="gene_abundances.tab"/> 436 <output name="gene_abundances" value="single_refgen_gene_abundances.bt.tab"/>
406 <output name="isoform_abundances" value="isoform_abundances.tab" /> 437 <output name="isoform_abundances" value="single_refgen_isoform_abundances.bt.tab" />
407 <output name="log"> 438 <output name="log">
408 <assert_contents> 439 <assert_contents>
409 <has_text text="Expression Results are written" /> 440 <has_text text="Expression Results are written" />
410 </assert_contents> 441 </assert_contents>
411 </output> 442 </output>
412 </test> 443 </test>
413 <test> 444 <test>
414 <param name="select_job" value="index"/> 445 <param name="select_job" value="index"/>
415 <param name="ref_type" value="genomic"/> 446 <param name="ref_type" value="genomic"/>
416 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> 447 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
417 <param name="gtf" value="ref.gtf" ftype="gtf"/> 448 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
418 <param name="reference_name" value="ref"/> 449 <param name="reference_name" value="alone"/>
419 <param name="select" value="No"/> 450 <param name="select" value="No"/>
420 <output name="reference_file"> 451 <output name="reference_file">
421 <assert_contents> 452 <assert_contents>
422 <has_text text="ref" /> 453 <has_text text="alone" />
423 </assert_contents> 454 </assert_contents>
424 </output> 455 </output>
425 </test> 456 </test>
426 </tests> 457 </tests>
427 458