# HG changeset patch
# User iuc
# Date 1733560831 0
# Node ID 2c3235c72ec14aa56a43a934c9c30d8a4b6598ef
# Parent  912de7fe289416b7bae8483f4b41bd395dd06901
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 3dd3145db6ed58efc3bf5f71e96515173967fc72

diff -r 912de7fe2894 -r 2c3235c72ec1 dada2_plotQualityProfile.xml
--- a/dada2_plotQualityProfile.xml	Mon Aug 07 01:30:59 2023 +0000
+++ b/dada2_plotQualityProfile.xml	Sat Dec 07 08:40:31 2024 +0000
@@ -89,10 +89,10 @@
         <data name="output" format="pdf" from_work_dir="output.pdf">
             <filter>batch_cond['paired_cond']['paired_select'] == "single"</filter>
         </data>
-        <data name="output_fwd" format="pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads">
+        <data name="output_fwd" format="pdf" default_identifier_source="batch_cond|paired_cond|reads" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads">
             <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
         </data>
-        <data name="output_rev" format="pdf" from_work_dir="output_rev.pdf" label="${tool.name} on ${on_string}: reverse reads">
+        <data name="output_rev" format="pdf" default_identifier_source="batch_cond|paired_cond|sdaer" from_work_dir="output_rev.pdf" label="${tool.name} on ${on_string}: reverse reads">
             <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
         </data>
     </outputs>
diff -r 912de7fe2894 -r 2c3235c72ec1 macros.xml
--- a/macros.xml	Mon Aug 07 01:30:59 2023 +0000
+++ b/macros.xml	Sat Dec 07 08:40:31 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 912de7fe2894 -r 2c3235c72ec1 test-data/gentest.R
--- a/test-data/gentest.R	Mon Aug 07 01:30:59 2023 +0000
+++ b/test-data/gentest.R	Sat Dec 07 08:40:31 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")