changeset 2:7dfcb39313d4 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit f65944aa0547c2fbe4b746cf443c85b2a76e9a48

--- a/dada2_primercheck.xml	Tue Feb 11 23:26:47 2025 +0000
+++ b/dada2_primercheck.xml	Sat Dec 20 14:13:18 2025 +0000
@@ -39,9 +39,6 @@
     #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
     #if $paired_cond.paired_select == "single"
         #set fwd_reads = $read
-    #elif $paired_cond.paired_select == "separate"
-        #set fwd_reads = $read
-        #set rev_reads = $paired_cond.sdaer[i]
     #else
         #set fwd_reads = $read.forward
         #set rev_reads = $read.reverse
@@ -49,9 +46,6 @@
     df <- rbind(df, c('$elid', 'FWD', 'FWD', sapply(FWD.orients, primerHits, fn = '$fwd_reads')))
     df <- rbind(df, c('$elid', 'REV', 'FWD', sapply(REV.orients, primerHits, fn = '$fwd_reads')))
     #if $paired_cond.paired_select != "single"
-        #if $paired_cond.paired_select == "separate"
-            #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.sdaer[i].element_identifier))
-        #end if
         df <- rbind(df, c('$elid', 'FWD', 'REV', sapply(FWD.orients, primerHits, fn = '$rev_reads')))
         df <- rbind(df, c('$elid', 'REV', 'REV', sapply(REV.orients, primerHits, fn = '$rev_reads')))
     #end if
@@ -104,23 +98,6 @@
                 </assert_contents>
             </output>
         </test>
-        <!-- paired data in separate collection -->
-        <test expect_num_outputs="1">
-            <conditional name="paired_cond">
-                <param name="paired_select" value="separate"/>
-                <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
-                <param name="sdaer" value="F3D0_S188_L001_R2_001.fastq.gz,F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
-            </conditional>
-
-            <param name="forward_primer" value="ACCTGCGGARGGATCA"/>
-            <param name="reverse_primer" value="GAGATCCRTTGYTRAAAGTT"/>
-            <output name="out">
-                <assert_contents>
-                    <has_n_lines n="9"/>
-                    <has_n_columns n="7"/>
-                </assert_contents>
-            </output>
-        </test>
         <!-- single end data -->
         <test expect_num_outputs="1">
             <conditional name="paired_cond">

--- a/macros.xml	Tue Feb 11 23:26:47 2025 +0000
+++ b/macros.xml	Sat Dec 20 14:13:18 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>