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comparison metaphlan2.xml @ 34:476d18d599c9 draft

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Uploaded
author bebatut
date Wed, 22 Feb 2017 09:19:47 -0500
parents e8206e14e889
children c312685a4b26
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33:e8206e14e889 34:476d18d599c9
43 --bowtie2_exe `which bowtie2` 43 --bowtie2_exe `which bowtie2`
44 44
45 #if $db.db_selector == "cached" 45 #if $db.db_selector == "cached"
46 #set $paths = dict([(_[0], _[3]) for _ in $db.cached_db.input.options.tool_data_table.data]) 46 #set $paths = dict([(_[0], _[3]) for _ in $db.cached_db.input.options.tool_data_table.data])
47 #set $db_choice = $db.cached_db.value 47 #set $db_choice = $db.cached_db.value
48 metadata=`ls $paths[$db_choice]/*.pkl` 48 --bowtie2db `ls $paths[$db_choice]/*.pkl | sed 's/\(.*\)\..*/\1/'`
49 --bowtie2db `echo $metadata | sed 's/\(.*\)\..*/\1/'` 49 --mpa_pkl `ls $paths[$db_choice]/*.pkl`
50 --mpa_pkl \$metadata
51 #else 50 #else
52 --bowtie2db 'ref_db/ref_db' 51 --bowtie2db 'ref_db/ref_db'
53 --mpa_pkl 'ref_db/metadata.pkl' 52 --mpa_pkl 'ref_db/metadata.pkl'
54 #end if 53 #end if
55 54