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comparison slamdunk.xml @ 3:17f54c2f4b0c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 11770937d250d7a332875becf06b9a42b17c46d1
author iuc
date Mon, 21 Jan 2019 16:46:31 -0500
parents 4b677ea9314a
children 40291a9a9c37
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2:4b677ea9314a 3:17f54c2f4b0c
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