From bad3c145ea30d2d29755ff6ea1776d537997b986 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Wed, 6 Nov 2019 08:16:54 +0100
Subject: [PATCH] dada2: fix data manager id and remove comments

---
 .../data_manager/dada2_fetcher.xml                |  2 +-
 tools/dada2/dada2_dada.xml                        | 15 +++++----------
 tools/dada2/dada2_filterAndTrim.xml               |  1 -
 tools/dada2/dada2_learnErrors.xml                 |  1 -
 4 files changed, 6 insertions(+), 13 deletions(-)

diff --git a/data_managers/data_manager_dada2/data_manager/dada2_fetcher.xml b/data_managers/data_manager_dada2/data_manager/dada2_fetcher.xml
index 7cc10155787..ce62153336d 100644
--- a/data_managers/data_manager_dada2/data_manager/dada2_fetcher.xml
+++ b/data_managers/data_manager_dada2/data_manager/dada2_fetcher.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="dada_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.7">
+<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.7">
     <description>Download reference databases</description>
     <command detect_errors="exit_code"><![CDATA[
     python '$__tool_directory__/data_manager.py'
diff --git a/tools/dada2/dada2_dada.xml b/tools/dada2/dada2_dada.xml
index 04ca9e43642..272be760cfc 100644
--- a/tools/dada2/dada2_dada.xml
+++ b/tools/dada2/dada2_dada.xml
@@ -42,8 +42,12 @@ pool <- F
 pool <- 'pseudo'
     #end if
 #end if
+
+## the Galaxy wrapper does not implement the arguments
+## - errorEstimationFunction = $errfoo, 
+## - selfConsist = $selfconsist
+## since they are probably not relevant for the end user
 dada_result <- dada(derep, err,
-## not needed for end user:    errorEstimationFunction = $errfoo, selfConsist = $selfconsist,
     pool = pool, multithread = nthreads)
 
 #if $batch_cond.batch_select == "no":
@@ -59,15 +63,6 @@ dada_result <- dada(derep, err,
 #else
     saveRDS(dada_result, file='$dada')
 #end if
-
-## for( id in names(dada_result) ){
-##     tab <- dada_result[[id]]\$clustering
-##     tabnames <- names(tab)
-##     tab\$sample <- id
-##     tabnames<-c("sample", tabnames)
-##     tab <- tab[,tabnames]
-##     write.table(tab, file = '$dada', append = T, quote = F, sep = "\t", row.names = F, col.names = F)
-## }
     ]]></configfile>
     </configfiles>
     <inputs>
diff --git a/tools/dada2/dada2_filterAndTrim.xml b/tools/dada2/dada2_filterAndTrim.xml
index 9a0cebec475..78d43417df2 100644
--- a/tools/dada2/dada2_filterAndTrim.xml
+++ b/tools/dada2/dada2_filterAndTrim.xml
@@ -8,7 +8,6 @@
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
 Rscript '$dada2_script'
-## && sed -i '1!b;s/^/#dataset/' $outtab
     ]]></command>
     <configfiles>
         <configfile name="dada2_script"><![CDATA[
diff --git a/tools/dada2/dada2_learnErrors.xml b/tools/dada2/dada2_learnErrors.xml
index e6b72023fce..2a420743053 100644
--- a/tools/dada2/dada2_learnErrors.xml
+++ b/tools/dada2/dada2_learnErrors.xml
@@ -26,7 +26,6 @@ err <- learnErrors(files, nbases = 10**$nbases,
            errorEstimationFunction = $advanced.errfoo, multithread = nthreads,
            randomize = $advanced.randomize, MAX_CONSIST = $advanced.maxconsist, OMEGA_C = $advanced.omegac)
 
-## write.table(err\$err_out, file = '$errors', quote = F, sep = "\t", row.names = T, col.names = F)
 saveRDS(err, file='$errors')
 
 ## generate error plots