#import re
        ## prepare inputs
        #if $init.start == "fasta":
            #set $infiles = ""
            #for $input in $init.input_fasta
                #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier))
                ln -s '$input' '${identifier}.fasta' &&
                #set $infiles = $infiles + str($identifier) + ","
            #end for
            #set $infiles = $infiles[:-1]
        #elif $init.start == "blast":
            #set $infilesbl = ""
            #for $input in $init.input_blast_out
                #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier))
                ln -s '$input' '$identifier' &&
                #set $infilesbl = $infilesbl + str($identifier) + ","
            #end for
            #set $infilesbl = $infilesbl[:-1]

            #set $infilesfa = ""
            #for $input in $init.input_blast_fa
                #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier))
                ln -s '$input' '$identifier' &&
                #set $infilesfa = $infilesfa + str($identifier) + ","
            #end for
            #set $infilesfa = $infilesfa[:-1]

            #set $identifier=re.sub('[^\w\-\s\.]', '_', str($init.specIDs.element_identifier))
            ln -s $init.specIDs $identifier &&

            #set $identifier=re.sub('[^\w\-\s\.]', '_', str($init.seqIDs.element_identifier))
            ln -s $init.seqIDs $identifier &&
        #end if

        ## start Orthofinder
        orthofinder
        #if $init.start == "fasta":
            -f .
            -S $init.search.search_program
            $init.input_type
        #elif $init.start == "blast":
            -b .
        #end if

        -I $inflation

        #if $trees.run_mode == "full":
            -M '${trees.tree_method.method}'
            #if $trees.tree_method.method == "msa":
                -A '${trees.tree_method.msa_program}'
                -T '${trees.tree_method.msa_tree_program}'
            #end if
        #else:
            $trees.run_mode
        #end if

        -t \${GALAXY_SLOTS:-1} -a \${GALAXY_SLOTS:-1} &&

        mv OrthoFinder/Results_* results
        #if $init.start == "fasta":
            #if $init.search.search_program == "blast":
                #if $init.search.keepblastout:
                    && mkdir -p results/WorkingDirectory/blast results/WorkingDirectory/fa &&
                    mv results/WorkingDirectory/Blast* results/WorkingDirectory/blast/ &&
                    mv results/WorkingDirectory/*.fa results/WorkingDirectory/fa/
                #end if
            #end if
        #end if