--- a/coverm_contig.xml	Wed Jul 26 07:35:24 2023 +0000
+++ b/coverm_contig.xml	Fri Aug 18 09:23:21 2023 +0000
@@ -231,6 +231,51 @@
             <conditional name="mapped">
                 <param name="mapped" value="not-mapped" />
                 <conditional name="mode">
+                    <param name="mode" value="individual"/>
+                    <conditional name="read_type">
+                        <param name="type" value="paired_collection"/>
+                        <param name="paired_reads">
+                            <collection type="paired">
+                                <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </param>
+                    </conditional>
+                    <param name="reference" value="7seqs.fna" />
+                    <param name="sharded" value="" />
+                </conditional>
+            </conditional>
+            <section name="alignment">
+                <param name="min_read_aligned_length" value="0" />
+                <param name="min_read_percent_identity" value="0" />
+                <param name="min_read_aligned_percent" value="0" />
+                <conditional name="proper_pairs_only">
+                    <param name="proper_pairs_only" value=""/>
+                </conditional>
+                <param name="exclude_supplementary" value=""/>
+            </section>
+            <section name="cov">
+                <param name="methods" value="mean"/>
+                <param name="trim_min" value="5"/>
+                <param name="trim_max" value="95"/>
+                <param name="min_covered_fraction" value="10"/>
+                <param name="contig_end_exclusion" value="75"/>
+            </section>
+            <param name="output_format" value="dense"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_text text="Contig"/>
+                    <has_text text="Mean"/>
+                    <has_text text="7seqs.fna"/>
+                    <has_text text="genome1~random_sequence_length_11000"/>
+                    <has_text text="genome2~seq1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="mapped">
+                <param name="mapped" value="not-mapped" />
+                <conditional name="mode">
                     <param name="mode" value="co"/>
                     <conditional name="read_type">
                         <param name="type" value="single"/>

--- a/macros.xml	Wed Jul 26 07:35:24 2023 +0000
+++ b/macros.xml	Fri Aug 18 09:23:21 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.6.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="requirements">
         <requirements>
@@ -118,9 +118,6 @@
             <option value="interleaved">Interleaved</option>
         </param>
     </xml>
-    <xml name="paired_reads">
-        <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
-    </xml>
     <xml name="individual_assembly_reads">
         <conditional name="read_type">
             <expand macro="read_type"/>
@@ -132,7 +129,7 @@
                 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" label="Reverse FASTA/Q file for mapping" />
             </when>
             <when value="paired_collection">
-                <expand macro="paired_reads"/>
+                <param name="paired_reads" type="data_collection" collection_type="paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
             </when>
             <when value="interleaved">
                 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" label="Interleaved FASTA/Q files for mapping" />
@@ -168,7 +165,7 @@
 ln -s '$reads.paired_reads.forward' '$fn' &&
             #set $fn = "rv/" + $id
             #silent $rv_fp.append( $fn )
-ln -s '$mreads.paired_reads.reverse' '${fn}' &&
+ln -s '$reads.paired_reads.reverse' '$fn' &&
         #else if $reads.type == 'interleaved'
             #set $fn = "interl/" + re.sub('[^\s\w\-\\.]', '_', str($reads.interleaved.element_identifier))
             #silent $interl_fp.append( $fn )
@@ -206,7 +203,7 @@
                 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" multiple="true" label="Reverse FASTA/Q file(s) for mapping" />
             </when>
             <when value="paired_collection">
-                <expand macro="paired_reads"/>
+                <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
             </when>
             <when value="interleaved">
                 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" multiple="true" label="Interleaved FASTA/Q files(s) for mapping" />
@@ -341,4 +338,4 @@
             <yield />
         </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>