# HG changeset patch
# User iuc
# Date 1766240053 0
# Node ID e8768ddeba329e4e9c905fb00b71c0422787299b
# Parent  00e0347751b1a2c0d174758d626aec80da387e64
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit f65944aa0547c2fbe4b746cf443c85b2a76e9a48

diff -r 00e0347751b1 -r e8768ddeba32 dada2_filterAndTrim.xml
--- a/dada2_filterAndTrim.xml	Tue Feb 11 23:27:12 2025 +0000
+++ b/dada2_filterAndTrim.xml	Sat Dec 20 14:14:13 2025 +0000
@@ -63,11 +63,6 @@
     rev <- c(rev, '$paired_cond.reads.reverse')
     filt.fwd <- c(filt.fwd, '$paired_output.forward')
     filt.rev <- c(filt.rev, '$paired_output.reverse')
-#else if $paired_cond.paired_select == "separate"
-    fwd <- c(fwd, '$paired_cond.reads')
-    rev <- c(rev, '$paired_cond.sdaer')
-    filt.fwd <- c(filt.fwd, '$output_fwd')
-    filt.rev <- c(filt.rev, '$output_rev')
 #else
     fwd <- c(fwd, '$paired_cond.reads')
     filt.fwd <- c(filt.fwd, '$output_single')
@@ -122,12 +117,6 @@
         <data name="output_single" format_source="paired_cond|reads" label="${tool.name} on ${on_string}: Reads" >
             <filter>paired_cond['paired_select'] == "single"</filter>
         </data>
-        <data name="output_fwd" format_source="paired_cond|reads" default_identifier_source="paired_cond|reads" label="${tool.name} on ${on_string}: Forward reads" >
-            <filter>paired_cond['paired_select'] == "separate"</filter>
-        </data>
-        <data name="output_rev" format_source="paired_cond|sdaer" default_identifier_source="paired_cond|sdaer" label="${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">
             <filter>output_statistics</filter>
         </data>
@@ -156,17 +145,6 @@
                 </assert_contents>
             </output>
         </test>
-        <!-- paired data given separately -->
-        <test expect_num_outputs="3">
-            <conditional name="paired_cond">
-                <param name="paired_select" value="separate"/>
-                <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
-                <param name="sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
-            </conditional>
-            <output name="output_fwd" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
-            <output name="output_rev" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
-            <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular"/>
-        </test>
         <!-- single end data -->
         <test expect_num_outputs="1">
             <conditional name="paired_cond">
@@ -177,7 +155,7 @@
             <param name="rmlowcomplex" value="2" />
             <param name="orientFwd" value="TACGG" />
             <param name="output_statistics" value="FALSE" />
-            <output name="output_fwd" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
+            <output name="output_single" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
         </test>
         <!-- single end data trimming -->
         <test expect_num_outputs="1">
@@ -190,7 +168,7 @@
             <param name="trim|trimRight" value="2" />
             <param name="trim|truncLen" value="2" />
             <param name="output_statistics" value="FALSE" />
-            <output name="output_fwd" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
+            <output name="output_single" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
         </test>
         <!-- single end data filtering -->
         <test expect_num_outputs="1">
@@ -204,7 +182,7 @@
             <param name="filter|minQ" value="13" />
             <param name="filter|maxEE" value="1" />
             <param name="output_statistics" value="FALSE" />
-            <output name="output_fwd" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
+            <output name="output_single" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
         </test>
         <!-- paired data w separate filters and trimmers for reverse -->
         <test expect_num_outputs="3">
diff -r 00e0347751b1 -r e8768ddeba32 macros.xml
--- a/macros.xml	Tue Feb 11 23:27:12 2025 +0000
+++ b/macros.xml	Sat Dec 20 14:14:13 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>