#if $task.task_selector != 'mbr'
                #if $task.msms_input.input_type_selector == "raw":
                    #set $format = '.raw'
                #else
                    #set $format = '.mzml'
                #end if
            #else:
                #set $format = '.tabular'
            #end if
        
        mkdir ./out &&
        #if $task.task_selector == "moff":
            
            mkdir ./ident_inputs &&
            #if $task.ident_input.input_type_selector == "ps":
                cp '$task.ident_input.ident_input_file' './ident_inputs/$task.ident_input.ident_input_file.element_identifier$format' &&
            #else
                cp '$task.ident_input.ident_input_file' ./tempfile1.tab &&
                ## optionally remove first line
                #if $task.ident_input.remove_header:
                    sed -i '1d' ./tempfile1.tab &&
                #end if
                ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
                echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > ./tempfile2.tab &&
                awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${task.ident_input.peptide}" prot="$task.ident_input.prot" mod="$task.ident_input.mod_peptide" rt="$task.ident_input.rt" mz="$task.ident_input.mz" mass="$task.ident_input.mass" charge="$task.ident_input.charge" ./tempfile1.tab >> ./tempfile2.tab &&
                mv ./tempfile2.tab './ident_inputs/$task.ident_input.ident_input_file.element_identifier$format' &&
            #end if
        
            
            mkdir ./raws &&
            ## for files, need to softlink the name to the history item
            ln -s '$task.msms_input.raw_list' './raws/$task.msms_input.raw_list.element_identifier$format' &&
        
            moff_all.py
                
            ## this is where the ident input gets passed to moff/moff_all/moff_mbr
            --tsv_list './ident_inputs/${task.ident_input.ident_input_file.element_identifier}$format'
        
                
            --raw_list './raws/$task.msms_input.raw_list.element_identifier$format'
        
                --tol $task.tol
                --mbr $task.mbr
                --xic_length $task.xic_length
                --rt_peak_win $task.rt_peak_win
                --rt_peak_win_match $task.rt_peak_win_match
	            --loc_out ./out
                    #if str( $task.match_filter.filter_flags ) == "filter":
                        --match_filter
                        --sample_size $task.match_filter.sample_size
                        --quantile_thr_filtering $task.match_filter.quantile_thr_filtering
                        #if ($task.match_filter.ptm_file):
                            --ptm_file '$task.match_filter.ptm_file'
                        #else:
                            --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json'
                        #end if
                    #end if
          #if ($task.peptide_summary):
              --peptide_summary
          #end if
          #if $task.peptide_summary:
              && mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
          #end if
          &&
          mv ./out/*moff_result.txt '$output_table'
          &&
          mv ./out/*.log '$output_logs'
        #else if $task.task_selector == "mbr":
           
            mkdir ./ident_inputs &&
            #if $task.ident_input.input_type_selector == "ps":
                #for $value in $task.ident_input.ident_input_file:
                    cp '${value}' './ident_inputs/${value.element_identifier}$format' &&
                #end for
            #else
                #for $i, $value in enumerate($task.ident_input.ident_input_file):
                    cp '${value}' './tempfile${i}_1.tab' &&
                    ## optionally remove first line
                    #if $task.ident_input.remove_header:
                        sed -i '1d' './tempfile${i}_1.tab' &&
                    #end if
                    ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
                    echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > './tempfile${i}_2.tab' &&
                    awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${task.ident_input.peptide}" prot="$task.ident_input.prot" mod="$task.ident_input.mod_peptide" rt="$task.ident_input.rt" mz="$task.ident_input.mz" mass="$task.ident_input.mass" charge="$task.ident_input.charge" './tempfile${i}_1.tab' >> './tempfile${i}_2.tab' &&
                    mv './tempfile${i}_2.tab' './ident_inputs/${value.element_identifier}$format' &&
                #end for
            #end if
        
           moff_all.py
                
            ## this is where the ident input gets passed to moff/moff_all/moff_mbr
            --tsv_list
            #for $value in $task.ident_input.ident_input_file:
                './ident_inputs/$value.element_identifier$format'
            #end for
        
                --mbr $task.mbr
				--raw_list
           &&
           mv ./mbr_output/* ./out
        #else:
           ## moff_all (mbr followed by apex)
           
            mkdir ./ident_inputs &&
            #if $task.ident_input.input_type_selector == "ps":
                cp '$task.ident_input.ident_input_file' './ident_inputs/$task.ident_input.ident_input_file.element_identifier$format' &&
            #else
                cp '$task.ident_input.ident_input_file' ./tempfile1.tab &&
                ## optionally remove first line
                #if $task.ident_input.remove_header:
                    sed -i '1d' ./tempfile1.tab &&
                #end if
                ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
                echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > ./tempfile2.tab &&
                awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${task.ident_input.peptide}" prot="$task.ident_input.prot" mod="$task.ident_input.mod_peptide" rt="$task.ident_input.rt" mz="$task.ident_input.mz" mass="$task.ident_input.mass" charge="$task.ident_input.charge" ./tempfile1.tab >> ./tempfile2.tab &&
                mv ./tempfile2.tab './ident_inputs/$task.ident_input.ident_input_file.element_identifier$format' &&
            #end if
        
           
            mkdir ./raws &&
            ## for files, need to softlink the name to the history item
            #for $value in $task.msms_input.raw_list:
                ln -s '$value' './raws/$value.element_identifier$format' &&
            #end for
        
           moff_all.py
               
            ## this is where the ident input gets passed to moff/moff_all/moff_mbr
            --tsv_list './ident_inputs/${task.ident_input.ident_input_file.element_identifier}$format'
        
               
            --raw_list
            #for $value in $task.msms_input.raw_list:
                './raws/$value.element_identifier$format'
            #end for
        
               --tol $task.tol
               --mbr $task.mbr
               --xic_length $task.xic_length
               --rt_peak_win $task.rt_peak_win
               --rt_peak_win_match $task.rt_peak_win_match
               --loc_out ./out
               #if ($task.peptide_summary):
                   --peptide_summary
               #end if
               #if str( $task.match_filter.filter_flags ) == "filter":
                    --match_filter
                    --sample_size $task.match_filter.sample_size
                    --quantile_thr_filtering $task.match_filter.quantile_thr_filtering
                    #if ($task.match_filter.ptm_file):
                        --ptm_file '$task.match_filter.ptm_file'
                    #else:
                        --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json'
                    #end if
               #end if

           #if $task.peptide_summary:
               && mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
		   #end if
	   #end if