Mercurial > repos > artbio > rsem
diff rsem-bwt2.xml @ 4:1823c8e07d96 draft
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 |
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--- a/rsem-bwt2.xml Tue Apr 03 18:25:39 2018 -0400 +++ b/rsem-bwt2.xml Fri Jun 01 03:00:34 2018 -0400 @@ -58,7 +58,7 @@ #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'): gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq && gunzip < '$run_rsem.input.fastq.fastq2' > uncomp_pair2.fastq && - #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'): + #elif $run_rsem.input.fastq.fastq1.is_of_type('fastq') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger'): ln -f -s '$run_rsem.input.fastq.fastq1' 'uncomp_pair1.fastq' && ln -f -s '$run_rsem.input.fastq.fastq2' 'uncomp_pair2.fastq' && #end if @@ -349,6 +349,7 @@ </assert_contents> </output> </test> + <!-- ungzipped paired-end fastqsanger --> <test> <param name="select_job" value="index"/> <param name="ref_type" value="genomic"/> @@ -388,19 +389,6 @@ </assert_contents> </output> </test> - <test> - <param name="select_job" value="index"/> - <param name="ref_type" value="genomic"/> - <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> - <param name="gtf" value="ref.gtf" ftype="gtf"/> - <param name="reference_name" value="ref"/> - <param name="select" value="No"/> - <output name="reference_file"> - <assert_contents> - <has_text text="ref" /> - </assert_contents> - </output> - </test> </tests> <help>