# HG changeset patch
# User iuc
# Date 1716550918 0
# Node ID 00f5005840fa416e157f5edbd62acb80f5ae7b07
# Parent  2cfceb9f9b8eb186bcda6f2ebdee17276772831e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 9bbc0898b9bbe73c7fc60ac162d80d749a7f97c1

diff -r 2cfceb9f9b8e -r 00f5005840fa dada2_dada.xml
--- a/dada2_dada.xml	Thu May 23 08:50:44 2024 +0000
+++ b/dada2_dada.xml	Fri May 24 11:41:58 2024 +0000
@@ -62,14 +62,18 @@
 #if $batch_cond.batch_select == "no":
     #if len($batch_cond.derep) > 1:
     for( id in names(dada_result) ){
+        print(id)
+        print(dada_result[[id]])
         saveRDS(dada_result[[id]], file=file.path("output" ,paste(id, "dada2_dada", sep=".")))
     }
     #else
     #for $d in $batch_cond.derep:
+        print(dada_result)
         saveRDS(dada_result, file=file.path("output" ,paste('$d.element_identifier', "dada2_dada", sep=".")))
     #end for
     #end if
 #else
+        print(dada_result)
     saveRDS(dada_result, file='$dada')
 #end if
     ]]></configfile>
@@ -116,6 +120,9 @@
                 <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
                 <element name="filterAndTrim_F3D141_R1.fq.gz" file="dada_F3D141_S207_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
             </output_collection>
+            <assert_stdout>
+                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
+            </assert_stdout>
         </test>
         <!-- default, batch -->
         <test expect_num_outputs="1">
@@ -123,6 +130,9 @@
             <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />
             <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
             <output name="dada" value="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada"  compare="sim_size" delta="10000"/>
+            <assert_stdout>
+                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
+            </assert_stdout>
        </test>
         <!-- test non-default options -->
         <test expect_num_outputs="1">
@@ -133,6 +143,9 @@
             <output_collection name="data_collection" type="list">
                 <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
             </output_collection>
+            <assert_stdout>
+                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
+            </assert_stdout>
         </test>
     </tests>
     <help><![CDATA[
diff -r 2cfceb9f9b8e -r 00f5005840fa macros.xml
--- a/macros.xml	Thu May 23 08:50:44 2024 +0000
+++ b/macros.xml	Fri May 24 11:41:58 2024 +0000
@@ -12,8 +12,8 @@
             <xref type="bioconductor">dada2</xref>
         </xrefs>
     </xml>
-    <token name="@DADA2_VERSION@">1.28</token>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@DADA2_VERSION@">1.30.0</token>
+    <token name="@WRAPPER_VERSION@">0</token>
 
     <xml name="version_command">
         <version_command><![CDATA[