#if $operation.to_perform == 'manipulate'
cp '${operation.loom}' converted.loom &&
python '$__tool_directory__/modify_loom.py' -f 'converted.loom'
    #if $operation.which_add.add_type == "cols":
    -a cols -c '${operation.which_add.cols}'
    #else if $operation.which_add.add_type == "rows":
    -a rows -r '${operation.which_add.rows}'
    #else if $operation.which_add.add_type == "layers":
    -a layers -l '${operation.which_add.layers}'
    #end if

#else if $operation.to_perform == 'export'
mkdir ./output &&
mkdir ./attributes &&
python '$__tool_directory__/loompy_to_tsv.py' -f '$operation.loom'

#else if $operation.to_perform == 'import'
    #if $operation.from.file_type == 'ad'

cat '$script_file' &&
python '$script_file'
    
    
    #else if $operation.from.file_type == 'tab'
python '$__tool_directory__/tsv_to_loompy.py'
    -c '${operation.coldata}'
    -r '${operation.rowdata}'
    -f '${operation.mainmatrix}'
        #if $operation.other_files
    '${operation.other_files}'
        #end if
    #end if
#end if