## Set up seqfile
        
        #if $aln_mode.aln_mode_select == 'interspecies':
            cat $aln_mode.in_tree >> seqfile.txt &&
        #end if
        #for $seq in $in_seqs:
            #set seq_fn = str($seq.label) + '.' + $seq.fasta.ext
            ln -s '$seq.fasta' '$seq_fn' &&
            printf '%s %s\n' '$seq.label' '$seq_fn' >> seqfile.txt 
            &&
        #end for

        ## Run cactus

        #if $aln_mode.aln_mode_select == 'intraspecies':
            ## Run cactus-pangenome
            ## --reference should be the first argument
            ## https://github.com/ComparativeGenomicsToolkit/cactus/issues/1093#issuecomment-1620088688
            cactus-pangenome 
            --reference $aln_mode.ref_level
            --binariesMode local
            --maxCores \${GALAXY_SLOTS:-4}
            --maxMemory \${GALAXY_MEMORY_MB:-16384}M    
            --outDir ./
            --outName alignment
            jobStore
            seqfile.txt
        #else if $aln_mode.aln_mode_select == 'interspecies':
            ## Run cactus normally
            cactus 
            --binariesMode local 
            --maxCores \${GALAXY_SLOTS:-4}
            --maxMemory \${GALAXY_MEMORY_MB:-16384}M
            --workDir ./
            jobStore
            seqfile.txt
            alignment.full.hal 
        #end if