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
date Sat, 02 Jun 2018 06:10:54 -0400
parents 1823c8e07d96
children 45a30e216fec
comparison
equal deleted inserted replaced
4:1823c8e07d96 5:835a2f3372b5
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