--- a/meryl.xml	Mon Jun 28 09:32:16 2021 +0000
+++ b/meryl.xml	Thu Aug 12 13:20:54 2021 +0000
@@ -15,12 +15,14 @@
             #elif $operation_type.options_kmer_size.kmer_size == 'provide'
                 #set size=$operation_type.options_kmer_size.input_kmer_size
             #end if
+            ln -s '$operation_type.input_reads' ./input.${operation_type.input_reads.ext} &&
+
             meryl
             $operation_type.count_operations
             k=$size
             memory=\$GALAXY_MEMORY_GB
             threads=\${GALAXY_SLOTS:-1}
-            $operation_type.input_reads
+            ./input.${operation_type.input_reads.ext}
             output read-db.meryl &&
             echo 'K-mer size: ${size}' &&
             tar -zcf read-db.meryldb read-db.meryl
@@ -176,17 +178,17 @@
                     <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly a threshold value</option>
                 </param>
                 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" />
-                
+
                 <conditional name="filter_type">
                     <param name="type" type="select" label="Type of filtering">
                         <option value="times">Return k-mers that occur N times in the input</option>
                         <option value="frequency">Return k-mers occurring at specific frequencies</option>
                     </param>
                     <when value="times">
-                        <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Number of times in the input" help="Return k-mers that occur N times in the input."/>
+                        <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Number of times in the input" help="Return k-mers that occur N times in the input." />
                     </when>
                     <when value="frequency">
-                        <param name="distinct" type="float" min="0" max="1" value="0.9998" optional="true" label="Frequency" help="Return k-mers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)"/>
+                        <param name="distinct" type="float" min="0" max="1" value="0.9998" optional="true" label="Frequency" help="Return k-mers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)" />
                     </when>
                 </conditional>
             </when>
@@ -326,7 +328,7 @@
                     <param name="distinct" value="0.9998" />
                 </conditional>
             </conditional>
-            <output name="read_db" ftype="meryldb" >
+            <output name="read_db" ftype="meryldb">
                 <assert_contents>
                     <has_size value="1634" delta="300" />
                 </assert_contents>
@@ -343,7 +345,7 @@
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="2621" delta="300"/>
+                    <has_size value="2621" delta="300" />
                 </assert_contents>
             </output>
         </test>
@@ -617,14 +619,14 @@
                 <param name="command_type" value="print" />
                 <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" />
             </conditional>
-            <output name="read_db_print" file="output_25.read-db.tabular" sort="True"/>
+            <output name="read_db_print" file="output_25.read-db.tabular" sort="true" />
         </test>
         <!--Test compressed files-->
         <test expect_num_outputs="1">
             <conditional name="operation_type">
                 <param name="command_type" value="count-kmers" />
                 <param name="count_operation" value="count" />
-                <param name="input_reads" value="child.fasta.gz" />
+                <param name="input_reads" value="child.fasta.gz" ftype="fasta.gz" />
                 <conditional name="options_kmer_size">
                     <param name="kmer_size" value="provide" />
                     <param name="input_kmer_size" value="7" />
@@ -632,7 +634,7 @@
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="1851" delta="300" />
+                    <has_size value="22200" delta="300" />
                 </assert_contents>
             </output>
             <assert_stdout>