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comparison rsem-bwt2.xml @ 4:1823c8e07d96 draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f
author artbio
date Fri, 01 Jun 2018 03:00:34 -0400
parents 26ead8419b63
children 835a2f3372b5
comparison
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3:26ead8419b63 4:1823c8e07d96
56 #end if 56 #end if
57 #elif $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="paired": 57 #elif $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="paired":
58 #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'): 58 #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'):
59 gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq && 59 gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq &&
60 gunzip < '$run_rsem.input.fastq.fastq2' > uncomp_pair2.fastq && 60 gunzip < '$run_rsem.input.fastq.fastq2' > uncomp_pair2.fastq &&
61 #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'): 61 #elif $run_rsem.input.fastq.fastq1.is_of_type('fastq') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger'):
62 ln -f -s '$run_rsem.input.fastq.fastq1' 'uncomp_pair1.fastq' && 62 ln -f -s '$run_rsem.input.fastq.fastq1' 'uncomp_pair1.fastq' &&
63 ln -f -s '$run_rsem.input.fastq.fastq2' 'uncomp_pair2.fastq' && 63 ln -f -s '$run_rsem.input.fastq.fastq2' 'uncomp_pair2.fastq' &&
64 #end if 64 #end if
65 #end if 65 #end if
66 rsem-calculate-expression 66 rsem-calculate-expression
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 -->
352 <test> 353 <test>
353 <param name="select_job" value="index"/> 354 <param name="select_job" value="index"/>
354 <param name="ref_type" value="genomic"/> 355 <param name="ref_type" value="genomic"/>
355 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> 356 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/>
356 <param name="gtf" value="ref.gtf" ftype="gtf"/> 357 <param name="gtf" value="ref.gtf" ftype="gtf"/>
386 <assert_contents> 387 <assert_contents>
387 <has_text text="ref" /> 388 <has_text text="ref" />
388 </assert_contents> 389 </assert_contents>
389 </output> 390 </output>
390 </test> 391 </test>
391 <test>
392 <param name="select_job" value="index"/>
393 <param name="ref_type" value="genomic"/>
394 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/>
395 <param name="gtf" value="ref.gtf" ftype="gtf"/>
396 <param name="reference_name" value="ref"/>
397 <param name="select" value="No"/>
398 <output name="reference_file">
399 <assert_contents>
400 <has_text text="ref" />
401 </assert_contents>
402 </output>
403 </test>
404 </tests> 392 </tests>
405 393
406 <help> 394 <help>
407 .. class:: infomark 395 .. class:: infomark
408 396