mkdir -p "./tmp_ppanggolin/msa" &&
        mkdir -p "./tmp_ppanggolin/tmpdir_msa" &&
        
        ppanggolin msa
        --pangenome '$pangenome_h5'
        --output ./tmp_ppanggolin/msa
        --tmpdir ./tmp_ppanggolin/tmpdir_msa
        --force
        --cpu "\${GALAXY_SLOTS:-4}"
        --disable_prog_bar
        --partition $choice_partition
        #if str($input_choose_partition.choice_partition) == "softcore"
            --soft_core $choice_soft_core
        #end if
        
        --source $choice_source
        $do_phylo
        $do_single_copy
        --translation_table $translation_table
        
        #set base_msa_source = "msa_" + str($input_choose_partition.choice_partition) + "_" + str($choice_source)
        #set base_genome_alignment = str($input_choose_partition.choice_partition) + "_genome_alignment.aln"
        #if str($input_choose_partition.choice_partition) == "softcore"
            #set base_genome_alignment = str($input_choose_partition.choice_partition) + "_" + str($choice_soft_core) + "_genome_alignment.aln"
        #end if
        
        && tar -cvf ./tmp_ppanggolin/msa/archive_${base_msa_source}.tar ./tmp_ppanggolin/msa/${base_msa_source}
        && gzip ./tmp_ppanggolin/msa/archive_${base_msa_source}.tar
        && mv ./tmp_ppanggolin/msa/archive_${base_msa_source}.tar.gz '${archive_msa_partition_source}'
        
        #if str($do_phylo) == "--phylo"
            && mv ./tmp_ppanggolin/msa/${base_genome_alignment} '${partition_genome_alignment}'
        #end if