--- a/quast.xml	Tue Nov 12 12:45:53 2024 +0000
+++ b/quast.xml	Sat Oct 04 15:48:40 2025 +0000
@@ -39,7 +39,7 @@
 
 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'
     #set $temp_ref_list_fp = 'temp_ref_list'
-    #for $i in $assembly.ref.references_list.split(',')
+    #for $i in str($assembly.ref.references_list).split(',')
     echo $i >> $temp_ref_list_fp &&
     #end for
 #end if
@@ -247,6 +247,10 @@
 #end if
     --threads \${GALAXY_SLOTS:-1}
 
+#if 'krona' not in $output_files or $assembly.ref.origin != 'silva'
+    --no-krona
+#end if
+
 #if $assembly.type == 'genome'
 && mkdir -p '$report_html.files_path'
 && cp outputdir/*.html '$report_html.files_path'
@@ -445,10 +449,10 @@
             <param argument="--local-mis-size" type="integer" value="200" optional="true" label="Minimal local misassembly size" help="Lower threshold for the local misassembly size. Shorter inconsistencies are considered as (long) indels. The default value is 200 bp. Note that the threshold should be equal to or lower than minimal extensive misassembly size, which is 1000 bp by default"/>
         </section>
         <section name="advanced" title="Advanced options">
-            <param argument="--contig-thresholds" type="text" value="0,1000" label="Comma-separated list of contig length thresholds (in bp)" help="Used in # contigs ≥ x and total length (≥ x) metrics"/>
+            <param argument="--contig-thresholds" type="text" value="0,1000,5000,10000,25000,50000" label="Comma-separated list of contig length thresholds (in bp)" help="Used in # contigs ≥ x and total length (≥ x) metrics"/>
             <param argument="--strict-NA" type="boolean" truevalue="--strict-NA" falsevalue="" checked="false" label="Break contigs at every misassembly event (including local ones) to compute NAx and NGAx statistics?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
             <param argument="--extensive-mis-size" type="integer" value="1000" min="85" label="Lower threshold for the relocation size (gap or overlap size between left and right flanking sequence)" help="Shorter relocations are considered as local misassemblies. It does not affect other types of extensive misassemblies (inversions and translocations). The default value is 1000 bp. Note that the threshold should be greater than maximum indel length which is 85 bp."/>
-            <param argument="--scaffold-gap-max-size" type="integer" value="1000" label="Max allowed scaffold gap length difference for detecting corresponding type of misassemblies" help="Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size"/>
+            <param argument="--scaffold-gap-max-size" type="integer" value="10000" label="Max allowed scaffold gap length difference for detecting corresponding type of misassemblies" help="Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size"/>
             <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
             <param argument="--skip-unaligned-mis-contigs" type="boolean" truevalue="" falsevalue="--skip-unaligned-mis-contigs" checked="true" label="Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
             <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size.Default value is 50. Note: requires --fragmented option" />
@@ -510,7 +514,7 @@
             <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
         </collection>
         <data name="krona" format="html" label="${tool.name} on ${on_string}:  Krona chart" from_work_dir="outputdir/krona_charts/*.html">
-            <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'none' and 'krona' in output_files</filter>
+            <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'silva' and 'krona' in output_files</filter>
         </data>
     </outputs>
     <tests>
@@ -1001,7 +1005,7 @@
                     <has_text text="# contigs (>= 0 bp)"/>
                     <has_text text="contig1"/>
                     <has_text text="# N's per 100 kbp"/>
-                    <has_n_lines n="22"/>
+                    <has_n_lines n="30"/>
                 </assert_contents>
             </output>
         </test>
@@ -1036,7 +1040,7 @@
                     <has_text text="# contigs (>= 0 bp)"/>
                     <has_text text="contig1"/>
                     <has_text text="# N's per 100 kbp"/>
-                    <has_n_lines n="15"/>
+                    <has_n_lines n="23"/>
                 </assert_contents>
             </output>
         </test>
@@ -1080,7 +1084,7 @@
                     <has_text text="# contigs (>= 0 bp)"/>
                     <has_text text="contigs1"/>
                     <has_text text="# N's per 100 kbp"/>
-                    <has_n_lines n="22"/>
+                    <has_n_lines n="30"/>
                 </assert_contents>
             </output>
         </test>