Mercurial > repos > iuc > hisat2
changeset 18:764756ab0eb5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
| author | iuc |
|---|---|
| date | Mon, 26 Mar 2018 17:23:52 -0400 |
| parents | 40e1083a4430 |
| children | fbf98f24097b |
| files | hisat2.xml |
| diffstat | 1 files changed, 12 insertions(+), 2 deletions(-) [+] |
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--- a/hisat2.xml Tue Nov 14 05:28:49 2017 -0500 +++ b/hisat2.xml Mon Mar 26 17:23:52 2018 -0400 @@ -233,8 +233,8 @@ --np ${adv.scoring_options.ambiguous_penalty} --rdg ${adv.scoring_options.read_open_penalty},${adv.scoring_options.read_extend_penalty} --rfg ${adv.scoring_options.ref_open_penalty},${adv.scoring_options.ref_extend_penalty} - --sp ${scoring_options.soft_clip_penalty_max},${adv.scoring_options.soft_clip_penalty_min} - --score-min ${scoring_options.function_type},${adv.scoring_options.constant_term},${adv.scoring_options.coefficient} + --sp ${adv.scoring_options.soft_clip_penalty_max},${adv.scoring_options.soft_clip_penalty_min} + --score-min ${adv.scoring_options.function_type},${adv.scoring_options.constant_term},${adv.scoring_options.coefficient} #end if @@ -575,6 +575,16 @@ <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> </test> + <!-- Ensure advanced scoring options work --> + <test expect_num_outputs="1" > + <param name="type" value="paired" /> + <param name="source" value="history" /> + <param name="history_item" ftype="fasta" value="phiX.fa" /> + <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> + <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> + <param name="adv|scoring_options|coefficient" value="-0.3"/> + <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> + </test> <!-- Ensure built-in reference works --> <test expect_num_outputs="1"> <param name="type" value="paired" />