# HG changeset patch
# User iuc
# Date 1752770272 0
# Node ID 3967889cda039153e5062877f115b62015b04aa4
# Parent  f73ab5187eed389eac19589296f298f9ba60bfa0
planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 4591c0ac5cf45b54e9fadb5d196ec3376b5b926f

diff -r f73ab5187eed -r 3967889cda03 macros.xml
--- a/macros.xml	Fri Aug 30 14:12:04 2024 +0000
+++ b/macros.xml	Thu Jul 17 16:37:52 2025 +0000
@@ -12,6 +12,6 @@
         </xrefs>
     </xml>
     <token name="@TOOL_VERSION@">2.3.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">20.05</token>
  </macros>
\ No newline at end of file
diff -r f73ab5187eed -r 3967889cda03 rna_quast.xml
--- a/rna_quast.xml	Fri Aug 30 14:12:04 2024 +0000
+++ b/rna_quast.xml	Thu Jul 17 16:37:52 2025 +0000
@@ -27,14 +27,14 @@
     #end if    
     mkdir outputdir &&
     rnaQUAST.py
-    --threads \${GALAXY_SLOTS:-8}
+    --threads "\${GALAXY_SLOTS:-8}"
     --transcripts
     #for $i in $transcripts
          '${re.sub('[^\w.]', '_', i.element_identifier)}'
     #end for
     #if $reads_option.selector == 'paired'
-        --left_reads '${reads_option.forward_reads}'
-        --right_reads '${reads_option.reverse_reads}'
+        --left_reads '${reads_option.paired_reads.forward}'
+        --right_reads '${reads_option.paired_reads.reverse}'
     #else if $reads_option.selector == 'single'
         --single_reads '${reads_option.single_reads}'
     #end if
@@ -117,17 +117,16 @@
         <param argument="--transcripts" type="data" format="fasta" multiple="true" label="Transcripts" help="File(s) with transcripts in FASTA format."/>
         <conditional name="reads_option">
             <param name="selector" type="select" label="Single-end or paired-end reads">
-                <option value="" selected="true">Disabled-end</option>
+                <option value="" selected="true">Disabled</option>
                 <option value="single" selected="true">Single-end</option>
                 <option value="paired">Paired-end (as individual datasets)</option>
             </param>
             <when value=""/>
             <when value="single">
-                <param format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" name="single_reads" type="data" label="RNA-Seq FASTQ/FASTA file"/>
+                <param format="fastqsanger,fastqsanger.gz" name="single_reads" type="data" label="RNA-Seq FASTQ file"/>
             </when>
             <when value="paired">
-                <param name="forward_reads" format="fastq,fastq.gz,fastqsanger ,fastqsanger.gz"  type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
-                <param name="reverse_reads" format="fastq,fastq.gz,fastqsanger, fastqsanger.gz"  type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/>
+                <param name="paired_reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Paired RNA-Seq FASTQ data"/> 
             </when>
         </conditional>
         <param argument="--reference" type="data" format="fasta" label="Reference genome"  multiple="true" optional="true" help="File with reference genome containing all chromosomes/scaffolds in FASTA forma." />
@@ -269,8 +268,7 @@
                 <param name="out_sr" value="tabular"/>
             </section>
             <conditional name="reads_option">
-                <param name="selector" value="single"/>
-                <param name="single_reads" value=""/>
+                <param name="selector" value=""/>
             </conditional>
             <output name="short_report_tabular" file="test_03_short_report.tab"/>
         </test>
@@ -307,8 +305,12 @@
             </section>
             <conditional name="reads_option">
                 <param name="selector" value='paired'/>
-                <param name="forward_reads" value="input_F.fastqsanger"/>
-                <param name="reverse_reads" value="input_F.fastqsanger"/>
+                <param name="paired_reads">
+                    <collection type="paired">
+                        <element name="forward" value="input_F.fastqsanger" ftype="fastqsanger"/>
+                        <element name="reverse" value="input_F.fastqsanger" ftype="fastqsanger"/>
+                    </collection>
+                </param>
             </conditional>
             <output name="short_report_tabular">
                 <assert_contents>
@@ -326,8 +328,12 @@
             </conditional>
             <conditional name="reads_option">
                 <param name="selector" value='paired'/>
-                <param name="forward_reads" value="input_F.fastqsanger"/>
-                <param name="reverse_reads" value="input_R.fastqsanger"/>
+                <param name="paired_reads">
+                    <collection type="paired">
+                        <element name="forward" value="input_F.fastqsanger" ftype="fastqsanger"/>
+                        <element name="reverse" value="input_R.fastqsanger" ftype="fastqsanger"/>
+                    </collection>
+                </param>
             </conditional>
             <section name="output_options">
                 <param name="out_sr" value="tabular"/>
@@ -356,8 +362,12 @@
             <param name="reference" value="reference.fasta"/>
             <conditional name="reads_option">
                 <param name="selector" value='paired'/>
-                <param name="forward_reads" value="input_F.fastqsanger"/>
-                <param name="reverse_reads" value="input_R.fastqsanger"/>
+                <param name="paired_reads">
+                    <collection type="paired">
+                        <element name="forward" value="input_F.fastqsanger" ftype="fastqsanger"/>
+                        <element name="reverse" value="input_R.fastqsanger" ftype="fastqsanger"/>
+                    </collection>
+                </param>
             </conditional>
             <conditional name="use_busco">
                 <param name="selector" value="true"/>
@@ -366,7 +376,7 @@
                     <param name="cached_db" value="busco-demo-db-20230328"/>
                 </conditional>
             </conditional>
-             <section name="output_options">
+            <section name="output_options">
                 <param name="out_sr" value="pdf,tabular"/>
                 <param name="out_add" value="fasta,gz"/>
             </section>
@@ -401,7 +411,9 @@
                     <param name="cached_db" value="busco-demo-db-20230328"/>
                 </conditional>
             </conditional>
-            <param name="out_add" value="complete,fasta,logs,gz"/>
+            <section name="output_options">
+                <param name="out_add" value="complete,fasta,logs,gz"/>
+            </section>
             <conditional name="reads_option">
                 <param name="selector" value="single"/>
                 <param name="single_reads" value="single_end.fastq.gz"/>
@@ -450,7 +462,9 @@
                     <param name="cached_db" value="busco-demo-db-20230328"/>
                 </conditional>
             </conditional>
-            <param name="out_add" value="complete,fasta,logs,gz"/>
+            <section name="output_options">
+                <param name="out_add" value="complete,fasta,logs,gz"/>
+            </section>
             <conditional name="reads_option">
                 <param name="selector" value="single"/>
                 <param name="single_reads" value="single_end.fastq.gz"/>