velvetg_wrapper.py
           '$input.extra_files_path'
           #if $generate_amos.afg  == "yes":
               -amos_file $generate_amos.afg
           #end if
           #if $unused_reads.generate_unused  == "yes":
               -unused_reads $unused_reads.generate_unused
           #end if
           $read_trkg
           #if $coverage.cutoff == "auto":
               -cov_cutoff auto
           #elif $coverage.cutoff == "value":
               -cov_cutoff $coverage.cov_cutoff
           #end if
           #if $expected.coverage == "auto":
               -exp_cov auto
           #elif $expected.coverage == "value":
               -exp_cov $expected.exp_cov
           #end if
           #if $contig_lgth.use_contig_lgth == "yes":
               -min_contig_lgth $contig_lgth.min_contig_lgth
           #end if
           #if $reads.paired == "yes":
               #if int($reads.ins_length) > 0:
                   -ins_length $reads.ins_length
               #end if
               #if $reads.options.advanced == "yes":
                   #if int($reads.options.ins_length_sd) > 0:
                       -ins_length_sd $reads.options.ins_length_sd
                   #end if
                   #if int($reads.options.ins_length2) > 0:
                       -ins_length2 $reads.options.ins_length2
                   #end if
                   #if int($reads.options.ins_length2_sd) > 0:
                       -ins_length2_sd $reads.options.ins_length2_sd
                   #end if
                   #if int($reads.options.ins_length_long) > 0:
                       -ins_length_long $reads.options.ins_length_long
                   #end if
                   #if int($reads.options.ins_length_long_sd) > 0:
                       -ins_length_long_sd $reads.options.ins_length_long_sd
                   #end if
                   #if int($reads.options.max_branch_length) > 0:
                       -max_branch_length $reads.options.max_branch_length
                   #end if
                   #if int($reads.options.max_divergence) > 0:
                       -max_divergence $reads.options.max_divergence
                   #end if
                   #if int($reads.options.max_gap_count) > 0:
                       -max_gap_count $reads.options.max_gap_count
                   #end if
                   #if int($reads.options.min_pair_count) > 0:
                       -min_pair_count $reads.options.min_pair_count
                   #end if
                   #if int($reads.options.max_coverage) > 0:
                       -max_coverage $reads.options.max_coverage
                   #end if
                   #if int($reads.options.long_mult_cutoff) > 0:
                       -long_mult_cutoff $reads.options.long_mult_cutoff
                   #end if
                   $reads.options.scaffolding
               #end if
           #end if