Mercurial > repos > iuc > slamdunk
comparison slamdunk.xml @ 3:24657d5edede draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 11770937d250d7a332875becf06b9a42b17c46d1
author | iuc |
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date | Mon, 21 Jan 2019 16:47:01 -0500 |
parents | fae4a5ec0653 |
children | 8b62f89924a7 |
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2:fae4a5ec0653 | 3:24657d5edede |
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19 #set $fastq_name = re.sub('[^\w\-\.]', '_', str($fastq.element_identifier)) | 19 #set $fastq_name = re.sub('[^\w\-\.]', '_', str($fastq.element_identifier)) |
20 ln -s '$fastq' './fastq/${fastq_name}' && | 20 ln -s '$fastq' './fastq/${fastq_name}' && |
21 #end for | 21 #end for |
22 | 22 |
23 slamdunk all -r reference.fa -b '$Reference' -o ./out | 23 slamdunk all -r reference.fa -b '$Reference' -o ./out |
24 -t \${GALAXY_SLOTS:-1} | |
24 -n $multimapper.multimappers | 25 -n $multimapper.multimappers |
25 $multimapper.multimap | 26 $multimapper.multimap |
26 #if $multimapper.filterbed.bedtofilter: | 27 #if $multimapper.filterbed.bedtofilter: |
27 -fb $multimapper.filterbed.bedtofilter | 28 -fb $multimapper.filterbed.bedtofilter |
28 #end if | 29 #end if |