Mercurial > repos > iuc > dada2_plotqualityprofile
changeset 8:fe1c3b7e4762 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 6248c33a4eacc8785cac321cd4603acf06fae0fd
| author | iuc |
|---|---|
| date | Thu, 23 May 2024 08:51:41 +0000 |
| parents | 7b8cb2b02978 |
| children | cae017b76acb |
| files | dada2_plotQualityProfile.xml macros.xml test-data/gentest.R |
| diffstat | 3 files changed, 13 insertions(+), 13 deletions(-) [+] |
line wrap: on
line diff
--- a/dada2_plotQualityProfile.xml Mon Aug 07 01:35:43 2023 +0000 +++ b/dada2_plotQualityProfile.xml Thu May 23 08:51:41 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>
--- a/macros.xml Mon Aug 07 01:35:43 2023 +0000 +++ b/macros.xml Thu May 23 08:51:41 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[
--- a/test-data/gentest.R Mon Aug 07 01:35:43 2023 +0000 +++ b/test-data/gentest.R Thu May 23 08:51:41 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")