comparison create_msp.R @ 28:be54f396ecfe draft default tip

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875

27:0d59d313d3f8

puritydf <- pa@puritydf





grped_df$fileid <- sapply(grped_df$filename, function(x) which(basename(pa@fileList)==x))

puritydf$fileid <- sapply(puritydf$filename, function(x) which(basename(pa@fileList)==x))

selfrag <- as.numeric(unique(grped_df$grpid)) 

of <- file(description = "outfile.msp", open = "w+a")

                idj <- paste(i,jj,sep=".")

                specj <- spec[[jj]]

                grpdj <- grpd[jj,]

                name = paste(i, grpdj$sample, grpdj$pid, sep='-')

                write.msp(name,grpdj$precurMtchMZ,"",specj,of)
            }

        }else{

            if (opt$mode=="max"){

                idx <- which(prec_int==max(prec_int))

                grpd <- grpd[idx,]
                name = paste(i, grpd$sample, grpd$pid, sep='-')
                write.msp(name,grpd$precurMtchMZ,"",specj[[idx]], of)
            }

            if (opt$mode=="average"){

        }
    }else{
        spec <- spec[[1]]

        grpd <- grped_df[j,]
        name = paste(i, grpd$sample, grpd$pid, sep='-')
        write.msp(name,grpd$precurMtchMZ,"",spec,of)
    }
}

28:be54f396ecfe

puritydf <- pa@puritydf



#grped_df$fileid <- sapply(grped_df$filename, function(x) which(basename(pa@fileList)==x))
#puritydf$fileid <- sapply(puritydf$filename, function(x) which(basename(pa@fileList)==x))




selfrag <- as.numeric(unique(grped_df$grpid)) 

of <- file(description = "outfile.msp", open = "w+a")

                idj <- paste(i,jj,sep=".")

                specj <- spec[[jj]]



                grpdj <- grpd[jj,]
                if ('sample' %in% colnames(grpd)){
                    fileid = grpdj$sample
                }else{
                    fileid = grpdj$fileid
                }
                name = paste(i, fileid, grpdj$pid, sep='-')

                write.msp(name,grpdj$precurMtchMZ,"",specj,of)
            }

        }else{

            if (opt$mode=="max"){

                idx <- which(prec_int==max(prec_int))

                grpd <- grpd[idx,]
                if ('sample' %in% colnames(grpd)){
                    fileid = grpd$sample
                }else{
                    fileid = grpd$fileid
                }

                name = paste(i, fileid, grpd$pid, sep='-')
                write.msp(name,grpd$precurMtchMZ,"",specj[[idx]], of)
            }

            if (opt$mode=="average"){

        }
    }else{
        spec <- spec[[1]]

        grpd <- grped_df[j,]
        if ('sample' %in% colnames(grpd)){
            fileid = grpd$sample
        }else{
            fileid = grpd$fileid
        }
        name = paste(i, fileid, grpd$pid, sep='-')
        write.msp(name,grpd$precurMtchMZ,"",spec,of)
    }
}