fix tests

Author: bernt-matthias

tools/quast/quast.xml

@@ -543,6 +543,7 @@ metaquast
                     </conditional>
                     <param name="circos" value="true"/>
                 </conditional>
+                <param name="min_identity" value="95.0"/>
                 <param name="orga_type" value=""/>
             </conditional>
             <param name="min_contig" value="500"/>
@@ -554,7 +555,6 @@ metaquast
                 </conditional>
                 <param name="rna_finding" value="true"/>
                 <param name="conserved_genes_finding" value="true"/>
-                <param name="min_identity" value="95.0"/>
             </section>
             <section name="alignments">
                 <param name="use_all_alignments" value="true"/>
@@ -568,7 +568,7 @@ metaquast
                 <param name="extensive_mis_size" value="1000"/>
                 <param name="scaffold_gap_max_size" value="1000"/>
                 <param name="unaligned_part_size" value="500"/>
-                <param name="skip_unaligned_mis_contigs" value="true"/>
+                <param name="skip_unaligned_mis_contigs" value="false"/>
                 <param name="fragmented_max_indent" value="50"/>
             </section>
             <param name="output_files" value="html"/>
@@ -655,7 +655,7 @@ metaquast
                 <param name="extensive_mis_size" value="1000"/>
                 <param name="scaffold_gap_max_size" value="1000"/>
                 <param name="unaligned_part_size" value="500"/>
-                <param name="skip_unaligned_mis_contigs" value="-"/>
+                <param name="skip_unaligned_mis_contigs" value="false"/>
             </section>
             <param name="output_files" value="html,pdf,log" />
             <output name="log" file="test3.log" ftype="txt" compare="sim_size"/>
@@ -677,6 +677,7 @@ metaquast
                     <param name="origin" value="silva"/>
                     <param name="max_ref_num" value="50"/>
                 </conditional>
+                <param name="min_identity" value="95.0"/>
             </conditional>
             <param name="min_contig" value="500"/>
             <param name="split_scaffolds" value="false"/>
@@ -691,7 +692,6 @@ metaquast
             <section name="alignments">
                 <param name="use_all_alignments" value="false"/>
                 <param name="min_alignment" value="65"/>
-                <param name="min_identity" value="95.0"/>
                 <param name="ambiguity_usage" value="one"/>
                 <param name="ambiguity_score" value="0.99"/>
                 <param name="fragmented" value="false"/>
@@ -702,7 +702,7 @@ metaquast
                 <param name="extensive_mis_size" value="1000"/>
                 <param name="scaffold_gap_max_size" value="1000"/>
                 <param name="unaligned_part_size" value="500"/>
-                <param name="skip_unaligned_mis_contigs" value="-"/>
+                <param name="skip_unaligned_mis_contigs" value="false"/>
             </section>
             <param name="output_files" value="log,html,tabular"/>
             <output name="log_meta" ftype="txt">
@@ -824,6 +824,7 @@ metaquast
             <conditional name="mode">
                 <param name="mode" value="co"/>
                 <conditional name="in">
+                    <param name="custom" value="true"/>
                     <repeat name="inputs">
                         <param name="input" value="meta_contigs_1.fasta"/>
                         <param name="labels" value="meta_contigs_1"/>
@@ -865,7 +866,7 @@ metaquast
                 <param name="extensive_mis_size" value="1000"/>
                 <param name="scaffold_gap_max_size" value="1000"/>
                 <param name="unaligned_part_size" value="500"/>
-                <param name="skip_unaligned_mis_contigs" value="-"/>
+                <param name="skip_unaligned_mis_contigs" value="false"/>
             </section>
             <param name="output_files" value="tabular,summary"/>
             <output name="report_tabular_meta" ftype="tabular">
@@ -884,6 +885,7 @@ metaquast
             <conditional name="mode">
                 <param name="mode" value="co"/>
                 <conditional name="in">
+                    <param name="custom" value="true"/>
                     <repeat name="inputs">
                         <param name="input" value="meta_contigs_1.fasta"/>
                         <param name="labels" value="meta_contigs_1"/>
@@ -925,7 +927,7 @@ metaquast
                 <param name="extensive_mis_size" value="1000"/>
                 <param name="scaffold_gap_max_size" value="1000"/>
                 <param name="unaligned_part_size" value="500"/>
-                <param name="skip_unaligned_mis_contigs" value="-"/>
+                <param name="skip_unaligned_mis_contigs" value="false"/>
             </section>
             <param name="output_files" value="html,log"/>
             <output name="report_html_meta" ftype="html">