Mercurial > repos > tomnl > create_sqlite_db

comparison frag4feature.R @ 3:2766f2a85997 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
author tomnl
date Fri, 30 Mar 2018 10:12:19 -0400
parents 1a88758357ed
children ff61a6fb23bf
comparison
equal deleted inserted replaced
2:3a3aab720f52 3:2766f2a85997
17 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]]) 17 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
18 galaxy_names <- galaxy_names[galaxy_names != ""] 18 galaxy_names <- galaxy_names[galaxy_names != ""]
19 19
20 nsave <- names(pa@fileList) 20 nsave <- names(pa@fileList)
21 old_filenames <- basename(pa@fileList) 21 old_filenames <- basename(pa@fileList)
22
22 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)] 23 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
23 names(pa@fileList) <- nsave 24 names(pa@fileList) <- nsave
24 25
25 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)]) 26 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
26 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)]) 27 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
27 } 28 }
28 29 print(pa@fileList)
30 print(xset@filepaths)
29 31
30 if(!all(basename(pa@fileList)==basename(xset@filepaths))){ 32 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
31 if(!all(names(pa@fileList)==basename(xset@filepaths))){ 33 if(!all(names(pa@fileList)==basename(xset@filepaths))){
32 print('FILELISTS DO NOT MATCH') 34 print('FILELISTS DO NOT MATCH')
33 message('FILELISTS DO NOT MATCH') 35 message('FILELISTS DO NOT MATCH')