# HG changeset patch
# User iuc
# Date 1766240270 0
# Node ID e7c2674e01fedf2d3a85582e968b09f81b711616
# Parent  4e469b758915dd70b604bd8cb16ee9830f533586
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit f65944aa0547c2fbe4b746cf443c85b2a76e9a48

diff -r 4e469b758915 -r e7c2674e01fe dada2_plotQualityProfile.xml
--- a/dada2_plotQualityProfile.xml	Tue Feb 11 23:28:03 2025 +0000
+++ b/dada2_plotQualityProfile.xml	Sat Dec 20 14:17:50 2025 +0000
@@ -23,9 +23,6 @@
         ln -s '$batch_cond.paired_cond.reads.forward' forward/'$elid' &&
         ln -s '$batch_cond.paired_cond.reads.reverse' reverse/'$elid' &&
     #end if
-    #if $batch_cond.paired_cond.paired_select == "separate"
-        ln -s '$batch_cond.paired_cond.sdaer' reverse/'$elid' &&
-    #end if
 #else
     #for $read in $batch_cond.paired_cond.reads:
         #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
@@ -36,12 +33,6 @@
             ln -s '$read.reverse' reverse/'$elid' &&
         #end if
     #end for
-    #if $batch_cond.paired_cond.paired_select == "separate"
-        #for $read in $batch_cond.paired_cond.sdaer:
-            #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
-            ln -s '$read' reverse/'$elid' &&
-        #end for
-    #end if
 #end if
 
     Rscript --slave '$dada2_script'
@@ -122,16 +113,6 @@
             <output name="output_fwd" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
             <output name="output_rev" value="qualityProfile_rev.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
         </test>
-        <!-- paired-separate joint, no-aggregate (sim_size because element ids differ) -->
-        <test expect_num_outputs="2">
-            <param name="batch_cond|batch_select" value="joint"/>
-            <param name="batch_cond|paired_cond|paired_select" value="separate"/>
-            <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
-            <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz,F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
-            <param name="batch_cond|aggregate" value="FALSE"/>
-            <output name="output_fwd" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
-            <output name="output_rev" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
-        </test>
         <!-- single, non-batch, aggregate, small sample -->
         <test expect_num_outputs="1">
             <param name="batch_cond|batch_select" value="joint"/>
@@ -155,15 +136,6 @@
             <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
             <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
         </test>
-        <!-- paired-separate batch  (sim_size because element ids differ)-->
-        <test expect_num_outputs="2">
-            <param name="batch_cond|batch_select" value="batch"/>
-            <param name="batch_cond|paired_cond|paired_select" value="separate"/>
-            <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
-            <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
-            <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
-            <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
-        </test>
         <!-- single, batch -->
         <test expect_num_outputs="1">
             <param name="batch_cond|batch_select" value="batch"/>
diff -r 4e469b758915 -r e7c2674e01fe macros.xml
--- a/macros.xml	Tue Feb 11 23:28:03 2025 +0000
+++ b/macros.xml	Sat Dec 20 14:17:50 2025 +0000
@@ -12,9 +12,9 @@
             <xref type="bioconductor">dada2</xref>
         </xrefs>
     </xml>
-    <token name="@PROFILE@">23.2</token>
+    <token name="@PROFILE@">24.2</token>
     <token name="@TOOL_VERSION@">1.34.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
 
     <xml name="version_command">
         <version_command><![CDATA[
@@ -80,17 +80,12 @@
     <xml name="fastq_input" token_multiple="" token_collection_type="" token_argument_fwd="" token_argument_rev="">
         <conditional name="paired_cond">
             <param name="paired_select" type="select" label="Paired reads">
-                <option value="paired">paired - in a data set pair</option>
-                <option value="separate">paired - in two separate data sets</option>
+                <option value="paired">paired</option>
                 <option value="single">single</option>
             </param>
             <when value="paired">
                 <param name="reads" argument="@ARGUMENT_FWD@/@ARGUMENT_REV@" type="data_collection" collection_type="@COLLECTION_TYPE@" format="fastq,fastq.gz" label="Paired short read data"/>
             </when>
-            <when value="separate">
-                <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Forward read data"/>
-                <param name="sdaer" argument="@ARGUMENT_REV@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Reverse read data"/>
-            </when>
             <when value="single">
                 <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Short read data"/>
             </when>