--- a/kma_map.xml	Fri Jun 14 21:15:44 2024 +0000
+++ b/kma_map.xml	Wed Jul 23 12:20:33 2025 +0000
@@ -10,11 +10,9 @@
     <command detect_errors="exit_code">
         <![CDATA[
         kma
-            -t \${GALAXY_SLOTS:-1}
+            -t "\${GALAXY_SLOTS:-1}"
             -t_db '${kma_index.fields.path}'
-            #if $single_paired.single_paired_selector == 'paired'
-                -ipe '${single_paired.forward_input}' '${single_paired.reverse_input}'
-            #elif $single_paired.single_paired_selector == "paired_collection":
+            #if $single_paired.single_paired_selector == "paired_collection":
                 -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
             #else:
                 -i '${single_paired.input_sequences}'
@@ -76,15 +74,10 @@
         <conditional name="single_paired">
             <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
                 <option value="paired_collection">Paired collection</option>
-                <option value="paired">Paired-end data</option>
                 <option selected="True" value="single">Single-end data</option>
             </param>
             <when value="paired_collection">
-                <param argument="-ipe" format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
-            </when>
-            <when value="paired">
-                <param argument="-ipe" format="@INTYPES@" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
-                <param argument="-ipe" format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
+                <param argument="-ipe" format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Paired reads" help="FASTQ datasets" />
             </when>
             <when value="single">
                 <param argument="-i" format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
@@ -138,10 +131,14 @@
     </outputs>
     <tests>
         <test expect_num_outputs="4">
-            <param name="single_paired_selector" value="single"/>
-            <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
-            <param name="advanced" value="advanced"/>
-            <param name="kmer_size" value="8"/>
+            <conditional name="single_paired">
+                <param name="single_paired_selector" value="single"/>
+                <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
+            </conditional>
+            <conditional name="settings">
+                <param name="advanced" value="advanced"/>
+                <param name="kmer_size" value="8"/>
+            </conditional>
             <param name="kma_index" value="test_index"/>
             <output name="result_overview" ftype="tabular">
                 <assert_contents>
@@ -174,15 +171,19 @@
             </output>
         </test>
         <test expect_num_outputs="5">
-            <param name="single_paired_selector" value="single"/>
-            <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
-            <param name="advanced" value="advanced"/>
-            <param name="kmer_size" value="8"/>
-            <param name="matrix" value="true"/>
+            <conditional name="single_paired">
+                <param name="single_paired_selector" value="single"/>
+                <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
+            </conditional>
+            <conditional name="settings">
+                <param name="advanced" value="advanced"/>
+                <param name="kmer_size" value="8"/>
+                <param name="matrix" value="true"/>
+            </conditional>
             <param name="kma_index" value="test_index"/>
             <output name="assembly_matrix" ftype="tabular">
                 <assert_contents>
-                    <has_n_lines n="2553"/>
+                    <has_n_lines n="2551"/>
                     <has_n_columns n="7" comment="#"/>
                     <has_line_matching expression="^A&#009;.*"/>
                     <has_line_matching expression="^T&#009;.*"/>
@@ -191,6 +192,51 @@
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="4">
+            <conditional name="single_paired">
+                <param name="single_paired_selector" value="paired_collection"/>
+                <param name="input_pair">
+                    <collection type="paired">
+                        <element name="forward" value="ERR884056_ecoli_b0842.mapped_R1.fastq.gz"/>
+                        <element name="reverse" value="ERR884056_ecoli_b0842.mapped_R1.fastq.gz"/>
+                    </collection>
+                </param>
+            </conditional>
+            <conditional name="settings">
+                <param name="advanced" value="advanced"/>
+                <param name="kmer_size" value="8"/>
+            </conditional>
+            <param name="kma_index" value="test_index"/>
+            <output name="result_overview" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="4"/>
+                    <has_n_columns n="11"/>
+                    <has_text text="#Template"/>
+                    <has_text text="b0842_1"/>
+                </assert_contents>
+            </output>
+            <output name="consensus_alignment" ftype="txt">
+                <assert_contents>
+                    <has_n_lines n="255"/>
+                    <has_text text="b0842_1"/>
+                    <has_text text="query" n="63"/>
+                    <has_text text="template" n="63"/>
+                </assert_contents>
+            </output>
+            <output name="consensus_sequences" ftype="fasta">
+                <assert_contents>
+                    <has_line_matching expression="^>.*" n="3"/>
+                    <has_line_matching expression="^>b0842_1"/>
+                </assert_contents>
+            </output>
+            <output name="read_mapping" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="1012"/>
+                    <has_n_columns n="7"/>
+                    <has_text text="b0842_1"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[