--- a/pima_report.xml	Fri Mar 10 16:35:16 2023 +0000
+++ b/pima_report.xml	Thu Mar 16 14:42:13 2023 +0000
@@ -36,6 +36,7 @@
 #end if
 
 mkdir amr_matrix_png_dir &&
+mkdir circos_png_dir &&
 mkdir feature_bed_dir &&
 mkdir feature_png_dir &&
 mkdir mutation_regions_dir &&
@@ -46,6 +47,11 @@
     #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
     ln -s $i 'amr_matrix_png_dir/$identifier' &&
 #end for
+#for $i in $circos_png:
+    #set file_name = $i.file_name
+    #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
+    ln -s $i 'circos_png_dir/$identifier' &&
+#end for
 #for $i in $features_bed:
     #set file_name = $i.file_name
     #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
@@ -74,6 +80,7 @@
 #if str($blastn_features) not in ['None', '']:
     --blastn_version '$blastn_version'
 #end if
+--circos_png_dir 'circos_png_dir'
 --compute_sequence_length_file '$compute_sequence_length_file'
 --contig_coverage_file '$contig_coverage_file'
 --dbkey '$aligned_sample.metadata.dbkey'
@@ -103,6 +110,7 @@
 --mutation_regions_bed_file '$mutation_regions_bed_file'
 --pima_css '${__tool_directory__}/pima.css'
 --plasmids_file '$plasmids_file'
+--quast_report_file '$quast_report_file'
 --reference_insertions_file '$reference_insertions_file'
 #if str($samtools_pileup_file) not in ['None', '']:
     --samtools_version '$samtools_version'
@@ -119,6 +127,7 @@
         <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
         <param name="bedtools_complementbed_file" type="data" format="bed" label="Bedtools ComplementBed BED file"/>
         <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular files"/>
+        <param name="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG files"/>
         <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
         <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
         <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
@@ -131,6 +140,7 @@
         <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
         <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
         <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
+        <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/>
         <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>
         <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/>
         <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/>