# HG changeset patch
# User iuc
# Date 1716454212 0
# Node ID 7434cc396c7bcf03905ef7b2d379795805929c3e
# Parent  addaf9d22850a1c3d0f0be6b3f25277eaf334e0d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 6248c33a4eacc8785cac321cd4603acf06fae0fd

diff -r addaf9d22850 -r 7434cc396c7b dada2_filterAndTrim.xml
--- a/dada2_filterAndTrim.xml	Mon Aug 07 01:36:09 2023 +0000
+++ b/dada2_filterAndTrim.xml	Thu May 23 08:50:12 2024 +0000
@@ -119,13 +119,13 @@
         <collection name="paired_output" type="paired" format_source="reads['forward']" label="${tool.name} on ${on_string}: Paired reads" >
             <filter>paired_cond['paired_select'] == "paired"</filter>
         </collection>
-        <data name="output_single" format_source="reads" label="${tool.name} on ${on_string}: Reads" >
+        <data name="output_single" format_source="paired_cond|reads" label="${tool.name} on ${on_string}: Reads" >
             <filter>paired_cond['paired_select'] == "single"</filter>
         </data>
-        <data name="output_fwd" format_source="reads" label="${tool.name} on ${on_string}: Forward reads" >
+        <data name="output_fwd" format_source="paired_cond|reads" default_identifier_source="paired_cond|reads" label="${tool.name} on ${on_string}: Forward reads" >
             <filter>paired_cond['paired_select'] == "separate"</filter>
         </data>
-        <data name="output_rev" format_source="sdaer" label="${tool.name} on ${on_string}: Reverse reads" >
+        <data name="output_rev" format_source="paired_cond|sdaer" default_identifier_source="paired_cond|sdaer" label="${tool.name} on ${on_string}: Reverse reads" >
             <filter>paired_cond['paired_select'] == "separate"</filter>
         </data>
         <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics">
diff -r addaf9d22850 -r 7434cc396c7b macros.xml
--- a/macros.xml	Mon Aug 07 01:36:09 2023 +0000
+++ b/macros.xml	Thu May 23 08:50:12 2024 +0000
@@ -13,7 +13,7 @@
         </xrefs>
     </xml>
     <token name="@DADA2_VERSION@">1.28</token>
-    <token name="@WRAPPER_VERSION@">0</token>
+    <token name="@WRAPPER_VERSION@">1</token>
 
     <xml name="version_command">
         <version_command><![CDATA[
diff -r addaf9d22850 -r 7434cc396c7b test-data/gentest.R
--- a/test-data/gentest.R	Mon Aug 07 01:36:09 2023 +0000
+++ b/test-data/gentest.R	Thu May 23 08:50:12 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")