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comparison metaphlan2.xml @ 33:e8206e14e889 draft

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Uploaded
author bebatut
date Wed, 22 Feb 2017 09:16:03 -0500
parents c941148c75c7
children 476d18d599c9
comparison
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32:c941148c75c7 33:e8206e14e889
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 #set $metadata = `ls $paths[$db_choice]/*.pkl` 48 metadata=`ls $paths[$db_choice]/*.pkl`
49 --bowtie2db $metadata[:-4] 49 --bowtie2db `echo $metadata | sed 's/\(.*\)\..*/\1/'`
50 --mpa_pkl '$metadata' 50 --mpa_pkl \$metadata
51 #else 51 #else
52 --bowtie2db 'ref_db/ref_db' 52 --bowtie2db 'ref_db/ref_db'
53 --mpa_pkl 'ref_db/metadata.pkl' 53 --mpa_pkl 'ref_db/metadata.pkl'
54 #end if 54 #end if
55 55