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comparison rsem.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
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>
360 <!-- test fastqsanger paired end -->
361 <param name="select_job" value="index"/>
362 <param name="ref_type" value="genomic"/>
363 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/>
364 <param name="gtf" value="ref.gtf" ftype="gtf"/>
365 <param name="reference_name" value="ref"/>
366 <param name="select" value="Yes"/>
367 <param name="sample" value="rsem_sample"/>
368 <param name="refSrc" value="self"/>
369 <param name="format" value="fastq"/>
370 <param name="matepair" value="paired"/>
371 <param name="fastq1" value="test2_forward.fastq" ftype="fastqsanger"/>
372 <param name="fastq2" value="test2_reverse.fastq" ftype="fastqsanger"/>
373 <param name="result_bams" value="none" />
374 <output name="reference_file">
375 <assert_contents>
376 <has_text text="ref" />
377 </assert_contents>
378 </output>
379 <output name="gene_abundances" value="de_gene_abundances.tab"/>
380 <output name="isoform_abundances" value="de_isoform_abundances.tab" />
381 <output name="log">
382 <assert_contents>
383 <has_text text="Expression Results are written" />
384 </assert_contents>
385 </output>
386 </test>
359 <test> 387 <test>
360 <param name="select_job" value="index"/> 388 <param name="select_job" value="index"/>
361 <param name="ref_type" value="genomic"/> 389 <param name="ref_type" value="genomic"/>
362 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> 390 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/>
363 <param name="gtf" value="ref.gtf" ftype="gtf"/> 391 <param name="gtf" value="ref.gtf" ftype="gtf"/>