Mercurial > repos > bebatut > metaphlan2

comparison metaphlan2.xml @ 38:4d1bf99ad5ef draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bebatut
date Mon, 27 Feb 2017 06:12:35 -0500
parents e7ed163633e1
children 99066fa0645b
comparison
equal deleted inserted replaced
37:e7ed163633e1 38:4d1bf99ad5ef
40 -o '$output_file' 40 -o '$output_file'
41 --input_type '${input_file.datatype.file_ext}' 41 --input_type '${input_file.datatype.file_ext}'
42 --bowtie2_exe `which bowtie2` 42 --bowtie2_exe `which bowtie2`
43 43
44 #if $db.db_selector == "cached" 44 #if $db.db_selector == "cached"
45 #set $path = ${db.cached_db.fields.path} 45 #set $path = $db.cached_db.fields.path
46 --bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'` 46 --bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'`
47 --mpa_pkl `ls $path/*.pkl` 47 --mpa_pkl `ls $path/*.pkl`
48 #else 48 #else
49 --bowtie2db 'ref_db/ref_db' 49 --bowtie2db 'ref_db/ref_db'
50 --mpa_pkl 'ref_db/metadata.pkl' 50 --mpa_pkl 'ref_db/metadata.pkl'