mkdir -p "./tmp_ppanggolin/all" &&
        mkdir -p "./tmp_ppanggolin/organism_list" &&
        mkdir -p "./tmp_ppanggolin/ln_input_genomes" &&
        
        touch "./tmp_ppanggolin/organism_list/organism.list" &&
        
        #set extension_input_files = ""
        #for $counter_input_files, $file in enumerate($genomes):
            #if $counter_input_files == 0:
            	#set extension_input_files = $file.ext
            #else:
                #if $file.ext != $extension_input_files:
                    #raise Exception("All the genome files must be of the same datatype, either all genbank files or all fasta files.")
            	#end if
            #end if
            
            #set base_name = str($file.element_identifier).replace(" ", "_")
            echo -e '${base_name}\t${file}' >> "./tmp_ppanggolin/organism_list/organism.list" &&
            
        #end for

        ppanggolin all

        #if $extension_input_files == "fasta":
            --fasta
        #elif $extension_input_files == "genbank":
            --anno
        #end if
        "./tmp_ppanggolin/organism_list/organism.list"
        
        -o ./tmp_ppanggolin/all
        --force
        --cpu "\${GALAXY_SLOTS:-4}"
        
        --coverage $coverage
        --identity $identity
        --translation_table $translation_table
        
        
        #if str($nb_of_partitions) != "":
            --nb_of_partitions $nb_of_partitions
        #end if
        
        $do_defrag
        

        #if "output_functional_modules" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/functional_modules.tsv > '${functional_modules}'
        #end if
        #if "output_modules_RGP_lists" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/modules_RGP_lists.tsv > '${modules_RGP_lists}'
        #end if
        #if "output_modules_spots" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/modules_spots.tsv > '${modules_spots}'
        #end if
        #if "output_modules_in_genomes" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/modules_in_genomes.tsv > '${modules_in_genomes}'
        #end if
        #if "output_modules_summary" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/modules_summary.tsv > '${modules_summary}'
        #end if
        #if "output_spot_borders" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/spot_borders.tsv > '${spot_borders}'
        #end if
        #if "output_spots" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/spots.tsv > '${spots}'
        #end if
        #if "output_summarize_spots" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/summarize_spots.tsv > '${summarize_spots}'
        #end if
        #if "output_border_protein_genes" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/border_protein_genes.fasta > '${border_protein_genes}'
        #end if
        
        #if "output_tile_plot" in $advanced_pangenome_optional_files:
        	&& cat ./tmp_ppanggolin/all/tile_plot.html > '${tile_plot}'
        #end if
        #if "output_ushaped_plot" in $advanced_pangenome_optional_files:
        	&& cat ./tmp_ppanggolin/all/Ushaped_plot.html > '${Ushaped_plot}'
        #end if
        
        #if "output_pangenomeGraph_json" in $advanced_pangenome_optional_files:
            && cat ./tmp_ppanggolin/all/pangenomeGraph.json > '${pangenomeGraph_json}'
        #end if
        #if "output_pangenomeGraph_gexf" in $advanced_pangenome_optional_files:
            && cat ./tmp_ppanggolin/all/pangenomeGraph.gexf > '${pangenomeGraph_gexf}'
        #end if
        #if "output_pangenomeGraph_light_gexf" in $advanced_pangenome_optional_files:
            && cat ./tmp_ppanggolin/all/pangenomeGraph_light.gexf > '${pangenomeGraph_light_gexf}'
        #end if
        
        #if "output_matrix" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/matrix.csv > '${matrix}'
        #end if
        #if "output_mean_persistent_duplication" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/mean_persistent_duplication.tsv > '${mean_persistent_duplication}'
        #end if
        #if "output_gene_families" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/gene_families.tsv > '${gene_families}'
        #end if
        #if "output_gene_presence_absence" in $advanced_pangenome_optional_files:
		&& cat ./tmp_ppanggolin/all/gene_presence_absence.Rtab > '${gene_presence_absence}'
        #end if
        
        
        && cat ./tmp_ppanggolin/all/regions_of_genomic_plasticity.tsv > '${regions_of_genomic_plasticity}'
        && cat ./tmp_ppanggolin/all/pangenome.h5 > '${pangenome_h5}'
        && cat ./tmp_ppanggolin/all/genomes_statistics.tsv > '${genomes_statistics}'