# HG changeset patch
# User iuc
# Date 1733560944 0
# Node ID 04dfd06326b1167e3b281812e5ca95348b339f5c
# Parent  0488001600380f01bfe28d31c4a00686f4dc73de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 3dd3145db6ed58efc3bf5f71e96515173967fc72

diff -r 048800160038 -r 04dfd06326b1 dada2_removeBimeraDenovo.xml
--- a/dada2_removeBimeraDenovo.xml	Mon Aug 07 01:28:51 2023 +0000
+++ b/dada2_removeBimeraDenovo.xml	Sat Dec 07 08:42:24 2024 +0000
@@ -100,7 +100,10 @@
 
 The frequency of chimeric sequences varies substantially from dataset to dataset, and depends on on factors including experimental procedures and sample complexity. Here chimeras make up about 21% of the merged sequence variants, but when we account for the abundances of those variants we see they account for only about 4% of the merged sequence reads.
 
-Considerations for your own data: Most of your reads should remain after chimera removal (it is not uncommon for a majority of sequence variants to be removed though). If most of your reads were removed as chimeric, upstream processing may need to be revisited. In almost all cases this is caused by primer sequences with ambiguous nucleotides that were not removed prior to beginning the DADA2 pipeline.
+Considerations for your own data: Most of your reads should remain after chimera removal (it is not uncommon for a majority of sequence variants to be removed though). If most of your reads were removed as chimeric, upstream processing may need to be revisited.
+In almost all cases this is caused by primer sequences with ambiguous nucleotides that were not removed prior to beginning the DADA2 pipeline.
+You can check for present primer sequences with the tool `dada2: primer check`
+
 
 @HELP_OVERVIEW@
     ]]></help>
diff -r 048800160038 -r 04dfd06326b1 macros.xml
--- a/macros.xml	Mon Aug 07 01:28:51 2023 +0000
+++ b/macros.xml	Sat Dec 07 08:42:24 2024 +0000
@@ -12,7 +12,7 @@
             <xref type="bioconductor">dada2</xref>
         </xrefs>
     </xml>
-    <token name="@DADA2_VERSION@">1.28</token>
+    <token name="@DADA2_VERSION@">1.30.0</token>
     <token name="@WRAPPER_VERSION@">0</token>
 
     <xml name="version_command">
diff -r 048800160038 -r 04dfd06326b1 test-data/gentest.R
--- a/test-data/gentest.R	Mon Aug 07 01:28:51 2023 +0000
+++ b/test-data/gentest.R	Sat Dec 07 08:42:24 2024 +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")