#import re
          ##PhyML outputs are based on input path and we need to create outputs in working_dir.
          #set input_name = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
          ln -sf '$input' '$input_name' &&
          #if $userInputTree
            #set userInputTree_name = re.sub('[^\s\w\-]', '_', str($userInputTree_name.element_identifier))
            ln -sf '$$userInputTree' '$userInputTree_name' && 
          #end if

          phyml --input '$input_name'
                ${phylip_format}
                --datatype '${seq.type_of_seq}'
                --multiple '${nb_data_set}'
                
                #if (str($support_condition.branchSupport) in ['0','-1','-2','-4','-5']):
                    --bootstrap '${support_condition.branchSupport}'
                #else:
                    --bootstrap '${support_condition.replicate}'
                #end if
                    
                --model '${seq.model}'
                #if $seq.type_of_seq == "nt":
                    -t '${seq.tstv}'
                #end if
            
                -f '${equi_freq}'
                --pinv '${prop_invar}'
                
                --nclasses '${nbSubstCat}'
                
                #if (str($nbSubstCat) != "1"):
                    --alpha '${gamma}'
                #end if

                --search '${move}'
                -o '${optimisationTopology}'
                
                #if $userInputTree:
                    --inputtree '${$userInputTree_name}'
                #end if
                
                #if $numStartSeed != "0":
                    --r_seed '${numStartSeed}'
                #end if
                
                --no_memory_check 
                | tee '${output_stdout}'