# HG changeset patch # User iuc # Date 1691372037 0 # Node ID 7136e9ab70db24f0277b960500a4ca0696e24a85 # Parent 1bc3657cd694597e9ab83549328f9dabde27a232 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit c2f6071f729b74540354f4a9e7084c9ac468a135 diff -r 1bc3657cd694 -r 7136e9ab70db dada2_removeBimeraDenovo.xml --- a/dada2_removeBimeraDenovo.xml Fri Jun 30 07:55:53 2023 +0000 +++ b/dada2_removeBimeraDenovo.xml Mon Aug 07 01:33:57 2023 +0000 @@ -33,15 +33,7 @@ write.data( seqtab.nochim, '$stable_mergepairs', "dada2_mergepairs" ) #end if -## dada input -if(class(unqs)=="list"){ - unqssum<-lapply(lapply(unqs, getUniques),sum) - outsum<-lapply(seqtab.nochim,sum) - mapply(function(X,Y) { 100*X/Y }, X=nonchimsum, Y=unqssum) - cat("remaining nonchimeric: ", mapply(function(X,Y) { 100*X/Y }, X=nonchimsum, Y=unqssum), "%") -}else{ - cat("remaining nonchimeric: ", 100*sum(getUniques(seqtab.nochim))/sum(getUniques(unqs)), "%") -} +cat("remaining nonchimeric: ", 100*sum(getUniques(seqtab.nochim))/sum(getUniques(unqs)), "%") ]]> diff -r 1bc3657cd694 -r 7136e9ab70db macros.xml --- a/macros.xml Fri Jun 30 07:55:53 2023 +0000 +++ b/macros.xml Mon Aug 07 01:33:57 2023 +0000 @@ -12,8 +12,8 @@ dada2 - 1.20 - 1 + 1.28 + 0 -
+
@@ -105,7 +106,7 @@
-
+
diff -r 1bc3657cd694 -r 7136e9ab70db test-data/gentest.R --- a/test-data/gentest.R Fri Jun 30 07:55:53 2023 +0000 +++ b/test-data/gentest.R Mon Aug 07 01:33:57 2023 +0000 @@ -11,9 +11,9 @@ print("filterAndTrim") for (i in seq_len(fwd)) { - ftout <- dada2::filterAndTrim(fwd[i], filt_fwd[i], rev[i], filt_rev[i]) - b <- paste(strsplit(fwd[i], ".", fixed = TRUE)[[1]][1], "tab", sep = ".") - write.table(ftout, b, quote = FALSE, sep = "\t", col.names = NA) + ftout <- dada2::filterAndTrim(fwd[i], filt_fwd[i], rev[i], filt_rev[i]) + b <- paste(strsplit(fwd[i], ".", fixed = TRUE)[[1]][1], "tab", sep = ".") + write.table(ftout, b, quote = FALSE, sep = "\t", col.names = NA) } # In the test only the 1st data set is used @@ -64,15 +64,15 @@ dada_fwd <- dada2::dada(filt_fwd, err_fwd) dada_rev <- dada2::dada(filt_rev, err_rev) for (id in sample_names) { - saveRDS(dada_fwd[[id]], file = paste("dada_", id, "_R1.Rdata", sep = "")) - saveRDS(dada_rev[[id]], file = paste("dada_", id, "_R2.Rdata", sep = "")) + saveRDS(dada_fwd[[id]], file = paste("dada_", id, "_R1.Rdata", sep = "")) + saveRDS(dada_rev[[id]], file = paste("dada_", id, "_R2.Rdata", sep = "")) } # merge pairs print("mergePairs") merged <- dada2::mergePairs(dada_fwd, filt_fwd, dada_rev, filt_rev) for (id in sample_names) { - saveRDS(merged[[id]], file = paste("mergePairs_", id, ".Rdata", sep = "")) + saveRDS(merged[[id]], file = paste("mergePairs_", id, ".Rdata", sep = "")) } @@ -85,8 +85,8 @@ df <- data.frame(length = as.numeric(names(reads_per_seqlen)), count = reads_per_seqlen) pdf("makeSequenceTable.pdf") ggplot(data = df, aes(x = length, y = count)) + - geom_col() + - theme_bw() + geom_col() + + theme_bw() bequiet <- dev.off() # remove bimera @@ -119,7 +119,7 @@ merged_nondef <- dada2::mergePairs(dada_fwd, filt_fwd, dada_rev, filt_rev, minOverlap = 8, maxMismatch = 1, justConcatenate = TRUE, trimOverhang = TRUE) for (id in sample_names) { - saveRDS(merged_nondef[[id]], file = paste("mergePairs_", id, "_nondefault.Rdata", sep = "")) + saveRDS(merged_nondef[[id]], file = paste("mergePairs_", id, "_nondefault.Rdata", sep = "")) } rb_dada_fwd <- dada2::removeBimeraDenovo(dada_fwd[["F3D0_S188_L001"]]) write.table(rb_dada_fwd, file = "removeBimeraDenovo_F3D0_dada_uniques.tab", quote = FALSE, sep = "\t", row.names = TRUE, col.names = FALSE) @@ -129,7 +129,7 @@ # SeqCounts get_n <- function(x) { - sum(dada2::getUniques(x)) + sum(dada2::getUniques(x)) } print("seqCounts ft")