dada2_filterandtrim: data2.R annotate

annotate data2.R @ 3:e4b415aa4c84 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty

author	matthias
date	Mon, 29 Apr 2019 08:57:57 -0400
parents	1d6e206b8291
children

rev	line source
0 1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	1 library(dada2)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	2
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	3 # library(DBI)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	4 # library(ggplot2)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	5 library(optparse)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	6 # library(RSQLite)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	7 # library(stringr)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	8
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	9 ## source required R functions
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	10 source('user_input_functions.R')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	11
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	12 # print dada2 version
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	13 print(paste("dada2 version: ", packageVersion("dada2")))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	14
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	15 # # R function to create fasta file from dada2 output data
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	16 # outdir is directory to output fasta file
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	17 # taxa is taxonomy file generated by dada2
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	18 # prefix is string for desired prefix attached to output file names
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	19
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	20 dada2fasta <- function(outdir, seqtab.nochim, prefix){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	21 seq <- colnames(seqtab.nochim)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	22 n <- 0
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	23 ASVs <- c()
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	24 for(i in seq){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	25 n <- n + 1
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	26 ASV <- paste('ASV', as.character(n), sep = '_')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	27 ASVs <- c(ASVs, ASV)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	28 line1 <- paste('>',ASV,sep='')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	29 write(line1, file.path(outdir,sprintf('%s.fasta',prefix)), append=T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	30 write(i, file.path(outdir,sprintf('%s.fasta',prefix)), append=T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	31 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	32 return(ASVs)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	33 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	34
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	35
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	36 # # R DADA2 workflow
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	37 # wd is path to fastq files
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	38 # r_path is path to user_input_functions.R
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	39 # outdir is path to output directory
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	40 # prefix is string for desired prefix attached to output file names
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	41
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	42 dada2run <- function(wd, r_path, outdir, prefix){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	43
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	44 # read-in files-------------------------------------------------------
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	45 ## obtain vectors of forward and reverse reads based on 'R1' and 'R2' in file names
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	46 ## additionally obtain the coressponding sample names for these files
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	47 p1 <- c()
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	48 p2 <- c()
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	49 sample.names <- c()
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	50 for(f in list.files(wd, full.names=T)){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	51 if(grepl('_1.fq', f)){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	52 sample <- gsub('^.[/](.?)_1\\.fq\\.gz', '\\1', f)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	53 sample.names <- c(sample.names, sample)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	54 p1 <- c(p1, f)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	55 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	56 if(grepl('_2.fq', f)){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	57 p2 <- c(p2, f)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	58 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	59 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	60 fnFs <- sort(p1)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	61 fnRs <- sort(p2)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	62 sample.names <- sort(sample.names)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	63
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	64 save(list = ls(all.names = TRUE), file = file.path(outdir, paste0(prefix, 'state_test.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	65 #load(file = file.path(outdir, paste0(prefix, 'state_test.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	66
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	67 ## print for review
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	68 to_view <- data.frame(sample.names, fnFs, fnRs)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	69 cat("The following fastq files were found:\n")
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	70 print(to_view)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	71
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	72 # Perform quality filtering and trimming---------------------------------
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	73 ## assign new names to samples
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	74 filtFs <- file.path(outdir, paste0(sample.names, 'F_filt.fastq.gz'))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	75 filtRs <- file.path(outdir, paste0(sample.names, 'R_filt.fastq.gz'))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	76
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	77 ## plot forward and reverse quality so that user can decide on filtering parameters
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	78 cat('Plotting quality profile of forward reads...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	79 Fqp1 <- plotQualityProfile(fnFs[1])
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	80 #print(Fqp1)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	81 ggsave(sprintf('%s_forward_1_qualityprofile.pdf',prefix), Fqp1, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	82 #ggsave(sprintf('%s_forward_1_qualityprofile.emf',prefix), Fqp1, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	83 Fqp2 <- plotQualityProfile(fnFs[2])
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	84 #print(Fqp2)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	85 ggsave(sprintf('%s_forward_2_qualityprofile.pdf',prefix),Fqp2, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	86 #ggsave(sprintf('%s_forward_2_qualityprofile.emf',prefix), Fqp2, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	87 #cat('Which position would you like to truncate the forward reads at?\nPlease use the red-dashed lines as a guide, where they stop appearing indicates good quality.\nNOTE: Do NOT over-trim! You still require overlap between your forward and reverse reads in order to merge them later!\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	88 len1 <- 240
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	89 cat('Plotting quality profile of reverse reads...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	90 Rqp1 <- plotQualityProfile(fnRs[1])
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	91 #print(Rqp1)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	92 ggsave(sprintf('%s_reverse_1_qualityprofile.pdf',prefix),Rqp1, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	93 #ggsave(sprintf('%s_reverse_1_qualityprofile.emf',prefix), Rqp1, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	94 Rqp2 <- plotQualityProfile(fnRs[2])
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	95 #print(Rqp2)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	96 ggsave(sprintf('%s_reverse_2_qualityprofile.pdf',prefix), Rqp2, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	97 #ggsave(sprintf('%s_reverse_2_qualityprofile.emf',prefix), Rqp2, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	98 #cat('Which position would you like to truncate the forward reads at?\nPlease use the red-dashed lines as a guide, where they stop appearing indicates good quality.\nNOTE: Do NOT over-trim! You still require overlap between your forward and reverse reads in order to merge them later!\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	99 len2 <- 240
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	100
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	101 ## filter and trim
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	102 ## remaining parameters set to recommended defaults
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	103 ## maxN must be set to 0 (DADA2 requries no Ns)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	104 ## The maxEE parameter sets the maximum number of "expected errors" allowed in a read, which is a better filter than simply averaging quality scores.
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	105 ## If not using Windows, you may set multithread to TRUE
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	106 ## NOTE: Do not use the truncLen parameter for ITS sequencing
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	107 ## trimLeft needs to be varied based on the size of your primers (i.e. it is used to trim your primer sequences)!!
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	108 cat('Filtering and trimming sequences...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	109 out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(len1,len2), maxN=0, maxEE=c(2,2), truncQ=2, rm.phix=T, compress=T, multithread=threads, trimLeft=15)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	110
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	111 ## have user review read count changes, and relax error rate if too many reads are lost
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	112 ## for example, you may especially want to relax the number of expected errors on the reverse reads (i.e. maxEE=c(2,5)), as the reverse is prone to error on the Illumina sequencing platform
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	113 print(head(out))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	114 check2 <- T
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	115 while(check2 == F){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	116 maxF <- numeric_input("What would you like the maximum number of expected errors in the forward reads to be?\nDefault 2:", 2)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	117 maxR <- numeric_input("What would you like the maximum number of expected errors in the reverse reads to be?\nDefault 5:", 5)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	118 out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(len1,len2), maxN=0, maxEE=c(maxF,maxR), truncQ=2, rm.phix=T, compress=T, multithread=threads)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	119 print(head(out))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	120 check2 <- yn_input('Proceed? If you lost too many reads, you can choose to not proceed and you will have the option to relax the error rate. Default yes:',T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	121 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	122
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	123 # Have DADA2 learn the error rates-----------------------------------------------
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	124 ## If not using Windows, you may set multithread to TRUE
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	125 read.subset <- 1e6
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	126 cat('Learning error rate of forward reads...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	127 errF <- learnErrors(filtFs, nreads=read.subset, multithread=threads)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	128
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	129 ## have user check estimated error rates
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	130 ## note the calculations are done with a subset of the total reads, as it is computationally intensive
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	131 ## if the fit is poor, the user has the option to try again with an increased subset number of reads
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	132 Error_f <- plotErrors(errF, nominalQ = T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	133 #print(Error_f)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	134 ggsave(sprintf('%s_forward_Error_plot.pdf',prefix), Error_f, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	135 #ggsave(sprintf('%s_forward_Error_plot.emf',prefix), Error_f, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	136 check3a <- T
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	137 while(check3a == F){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	138 read.subset <- numeric_input('Please specify the number of reads you would like dada2 to utilize to calculate the error rate.\nThe default previously used was 1e6.\nThe newly recommended default is 10-fold greater,\n1e7:',1e7)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	139 errF <- learnErrors(filtFs, nreads=read.subset, multithread=threads)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	140 print(Error_f)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	141 ggsave(sprintf('%s_forward_Error_plot.pdf',prefix), path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	142 ggsave(sprintf('%s_forward_Error_plot.emf',prefix), path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	143 check3a <- yn_input('Proceed?\nThe estimated error rate (black line) should fit to the observed error rates for each consensus quality score (black points).\nAdditionally, the error rates expected under the nominal definition of the Q-value (quality score) should decrease as the quality score increases (or flat-line).\nIf you do not have a good fit, you may want dada2 to re-learn the error rates with a higher number of reads in the utilized subset.\nA subset of reads is always used as the algorithm is computationally intensive.\nDefault yes:',T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	144 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	145
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	146
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	147 ## also do for reverseL
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	148 cat('Learning error rate of reverse reads...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	149 errR <- learnErrors(filtRs, nreads=read.subset, multithread=threads)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	150 Error_r <- plotErrors(errR, nominalQ=T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	151 #print(Error_r)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	152 ggsave(sprintf('%s_reverse_Error_plot.pdf',prefix), Error_r, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	153 #ggsave(sprintf('%s_reverse_Error_plot.emf',prefix), Error_r, path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	154 check3b <- T
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	155 while(check3b == F){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	156 read.subset <- numeric_input('Please specify the number of reads you would like dada2 to utilize to calculate the error rate.\nThe default previously used was 1e6.\nThe newly recommended default is 10-fold greater,\n1e7:',1e7)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	157 errR <- learnErrors(filtRs, nreads=read.subset, multithread=threads)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	158 print(Error_r)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	159 ggsave(sprintf('%s_reverse_Error_plot.pdf',prefix), path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	160 #ggsave(sprintf('%s_reverse_Error_plot.emf',prefix), path = outdir, width = 20,height = 15,units = c("cm"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	161 check3b <- yn_input('Proceed?\nThe estimated error rate (black line) should fit to the observed error rates for each consensus quality score (black points).\nAdditionally, the error rates expected under the nominal definition of the Q-value (quality score) should decrease as the quality score increases (or flat-line).\nIf you do not have a good fit, you may want dada2 to re-learn the error rates with a higher number of reads in the utilized subset.\nA subset of reads is always used as the algorithm is computationally intensive.\nDefault yes:',T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	162 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	163
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	164 save(list = ls(all.names = TRUE), file = file.path(outdir, paste0(prefix, 'state_post_learning.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	165 #load(file = file.path(outdir, paste0(prefix, 'state_post_learning.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	166
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	167 # Dereplicate sequences to generate unique sequence fastq files with corresponding count tables-------------------------
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	168 ## NOTE: if your dataset is huge, you may run out of RAM. Please see https://benjjneb.github.io/dada2/bigdata.html for details.
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	169 cat('Dereplicating forward reads...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	170 derepFs <- derepFastq(filtFs, verbose=T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	171 cat('Dereplicating reverse reads...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	172 derepRs <- derepFastq(filtRs, verbose=T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	173
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	174 ## name the derep-class objects by sample names
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	175 names(derepFs) <- sample.names
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	176 names(derepRs) <- sample.names
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	177
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	178 save(list = ls(all.names = TRUE), file = file.path(outdir, paste0(prefix, 'state_post_derep.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	179 #load(file = file.path(outdir, paste0(prefix, 'state_post_derep.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	180
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	181 # Infer sequence variants using learned error rates---------------------------------
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	182 ## If not using Windows, you may set multithread to TRUE
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	183 ## NOTE: if your dataset is huge, you may run out of RAM. Please see https://benjjneb.github.io/dada2/bigdata.html for details.
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	184 ## NOTE2: you can use DADA2 for 454 or IonTorrent data as well. Please see https://benjjneb.github.io/dada2/tutorial.html.
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	185 s.pool = F
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	186 cat('Inferring sequence variants of forward reads...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	187 dadaFs <- dada(derepFs, err=errF, pool=s.pool, multithread=threads)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	188
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	189 ## have user inspect detected number of sequence variants, to ensure it is logical based on the biological context of their samples
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	190 ## if you have low sampling depths, you may not want to process each sample independently as per default, but set pool=T. It gives better results at increased computation time. The user will have the option to do this if the number of sequence variants doesn't make sense.
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	191 print(dadaFs[[1]])
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	192 check4 <- T
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	193 if(check4 == F){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	194 s.pool = T
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	195 dadaFs <- dada(derepFs, err=errF, pool=s.pool, multithread=threads)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	196 print(dadaFs[[1]])
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	197 cat('Hopefully, these results make more sense.\nOtherwise, there is not much more you can do except start over!\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	198 check <- yn_input('Proceed? Default yes, no to quit:',T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	199 if(check == F){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	200 stop()
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	201 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	202 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	203
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	204 ## also do for reverse, but don't need to re-check as you need to keep the pool consistent between the forward and reverse!
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	205 cat('Inferring sequence variants of reversed reads...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	206 dadaRs <- dada(derepRs, err=errR, pool=s.pool, multithread=threads)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	207
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	208 save(list = ls(all.names = TRUE), file = file.path(outdir, paste0(prefix, 'state_post_dada.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	209 #load(file = file.path(outdir, paste0(prefix, 'state_post_dada.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	210
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	211
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	212 # Merge forward and reverse reads-------------------------------------------------
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	213 cat('Merging paired-end reads...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	214 mergers <- mergePairs(dadaFs, derepFs, dadaRs, derepRs, verbose=T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	215 #cat('Most of your reads should have been retained (i.e. were able to merge, see above).\nOtherwise, there is not much more you can do except start over (i.e. did you over-trim your sequences??)!\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	216 check <- T
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	217 if(check == F){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	218 stop()
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	219 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	220
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	221 # Construct sequences table-------------------------------------------------------
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	222 cat('Constructing sequence table...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	223 seqtab <- makeSequenceTable(mergers)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	224
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	225 save(list = ls(all.names = TRUE), file = file.path(outdir, paste0(prefix, 'state_post_merge.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	226 #load(file = file.path(outdir, paste0(prefix, 'state_post_merge.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	227
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	228
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	229 ## inspect distribution of sequence lengths
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	230 ## give user the option to filter out overly long or short sequneces
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	231 cat('Sequence length distribution listed below:\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	232 print(table(nchar(getSequences(seqtab))))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	233 check5 <- T
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	234 if(check5 == F){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	235 min.cutoff <- numeric_input('Please input desired minimum length of sequences:',NULL)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	236 max.cutoff <- numeric_input('Please input desired maximum length of sequences:',NULL)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	237 seqtab <- seqtab[,nchar(colnames(seqtab)) %in% seq(min.cutoff,max.cutoff)]
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	238 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	239
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	240 # Remove chimeras------------------------------------------------------------------
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	241 ## If not using Windows, you may set multithread to TRUE
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	242 cat('Removing chimeras...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	243 seqtab.nochim <- removeBimeraDenovo(seqtab, method='consensus', multithread=threads, verbose=T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	244
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	245 ## display percentage of chimeras removed
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	246 ## this number should be small (<5%), otherwise some processing parameters need to be revisited
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	247 percent.nochim <- (sum(seqtab.nochim)/sum(seqtab))*100
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	248 percent.nochim <- paste(as.character(percent.nochim),'of reads retained after chimera removal.\n',sep=' ')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	249 cat(percent.nochim)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	250 #cat('Most of your reads should have been retained.\nOtherwise, there is not much more you can do except start over!\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	251 check <- T
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	252 if(check == F){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	253 stop()
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	254 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	255
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	256 # Final sanity check--------------------------------------------------------------
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	257 ## track reads removed throughout the pipeline
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	258 ## If processing a single sample, remove the sapply calls: e.g. replace sapply(dadaFs, getN) with getN(dadaFs)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	259 getN <- function(x) sum(getUniques(x))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	260 track <- cbind(out, sapply(dadaFs, getN), sapply(mergers, getN), rowSums(seqtab), rowSums(seqtab.nochim))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	261 colnames(track) <- c("input", "filtered", "denoised", "merged", "tabled", "nonchim")
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	262 rownames(track) <- sample.names
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	263 print(head(track))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	264 #cat('Most of your reads should have been retained.\nOtherwise, there is not much more you can do except start over!\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	265 check <- T
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	266 if(check == F){
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	267 stop()
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	268 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	269
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	270 write.csv(track,file=file.path(outdir, sprintf('%s_read_count-quality_control.csv',prefix)))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	271
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	272 save(list = ls(all.names = TRUE), file = file.path(outdir, paste0(prefix, 'state_post_chimera.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	273 # load(file = file.path(outdir, paste0(prefix, 'state_post_chimera.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	274
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	275 # Assign taxonomy-----------------------------------------------------------------
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	276 ## require silva database files
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	277 ## If not using Windows, you may set multithread to TRUE
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	278 ## Minimum boot strap should be 80, but for sequnce length =< 250 Minimum bootstrap set to 50 (which is also the default)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	279
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	280 ## SILVA
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	281 cat('Assigning taxonomy to genus level using SILVA...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	282 taxa_silva <- assignTaxonomy(seqtab.nochim, file.path(wd,"silva_nr_v132_train_set.fa.gz"), multithread=threads, minBoot=80, tryRC=T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	283 cat('Assigning taxonomy at species level using SILVA...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	284 taxa_silva <- addSpecies(taxa_silva, file.path(wd,"silva_species_assignment_v132.fa.gz"), allowMultiple=T, tryRC=T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	285 write.csv(taxa_silva,file=file.path(outdir, sprintf('%s_taxonomy_silva.csv',prefix)))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	286
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	287 ## RDP - used for copy number correction
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	288 cat('Assigning taxonomy to genus level using RDP...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	289 taxa_rdp <- assignTaxonomy(seqtab.nochim, file.path(wd,"rdp_train_set_16.fa.gz"), multithread=threads, minBoot=80, tryRC=T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	290 cat('Assigning taxonomy at species level using RDP...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	291 taxa_rdp <- addSpecies(taxa_rdp, file.path(wd,"rdp_species_assignment_16.fa.gz"), allowMultiple=T, tryRC=T)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	292 write.csv(taxa_rdp,file=file.path(outdir, sprintf('%s_taxonomy_rdp.csv',prefix)))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	293 save(list = ls(all.names = TRUE), file = file.path(outdir, paste0(prefix, 'state_post_tax.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	294 #load(file = file.path(outdir, paste0(prefix, 'state_post_tax.Rdata')))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	295
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	296
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	297 # Return data----------------------------------------------------------------------
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	298 cat('Returning data...\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	299 ## create fasta file
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	300 ASVs <- dada2fasta(outdir, seqtab.nochim, prefix)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	301 ## create master dataframe for each classification
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	302
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	303 ## Assigning ASVs to count table
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	304 sequences <- colnames(seqtab.nochim)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	305 colnames(seqtab.nochim) <- ASVs
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	306 seqtab.nochim <- t(seqtab.nochim)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	307
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	308 ## silva
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	309 taxa_silva <- taxa_silva[match(sequences, rownames(taxa_silva)),]
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	310 rownames(taxa_silva) <- ASVs
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	311 d <- merge(seqtab.nochim, taxa_silva, by='row.names')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	312 colnames(d)[1] <- 'ASV'
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	313 ## create database of all information
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	314 db <- dbConnect(RSQLite::SQLite(), file.path(outdir, sprintf('%s.sqlite',prefix)))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	315 dbWriteTable(db, 'dada2_results_silva', d)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	316 ## write master dataframe for user, and return it
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	317 write.table(d, file.path(outdir, sprintf('%s_dada2_results_silva.txt',prefix)), sep='\t', quote=F, row.names=F)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	318
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	319 ## rdp
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	320 taxa_rdp <- taxa_rdp[match(sequences, rownames(taxa_rdp)),]
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	321 rownames(taxa_rdp) <- ASVs
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	322 d <- merge(seqtab.nochim, taxa_rdp, by='row.names')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	323 colnames(d)[1] <- 'ASV'
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	324 ## create database of all information
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	325 dbWriteTable(db, 'dada2_results_rdp', d)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	326 dbDisconnect(db)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	327 ## write master dataframe for user, and return it
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	328 write.table(d, file.path(outdir, sprintf('%s_dada2_results_rdp.txt',prefix)), sep='\t', quote=F, row.names=F)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	329 return(d)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	330
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	331 cat('DADA2 processing completed!\n')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	332 }
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	333
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	334
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	335 option_list = list(
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	336 make_option(c("-t", "--threads"), type = "integer", default = 1,
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	337 help = "number of threads to use", metavar = "THREADS")
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	338 );
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	339
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	340 opt_parser = OptionParser(option_list=option_list);
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	341 opt = parse_args(opt_parser);
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	342
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	343 print(opt)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	344
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	345 threads = as.integer(Sys.getenv("NSLOTS", "1"))
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	346
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	347 exit(1)
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	348
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	349
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	350
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	351 dada2run(wd='/work/haange/Leaky_gut/', r_path='/work/haange/Leaky_gut', outdir='/work/haange/Leaky_gut/results', prefix='Leaky_gut')
1d6e206b8291 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty matthias parents: diff changeset	352

Mercurial > repos > matthias > dada2_filterandtrim

annotate data2.R @ 3:e4b415aa4c84 draft