cd-hit$est.est_select$twod.twod_select
-i '$fasta_in'
-o rep_seq
-c $est.similarity
-n $est.wordsize
#if $est.est_select == '-est':
    $est.strand
    #if str($est.estadvalign.mask) != 'None':
        -mask '$est.estadvalign.mask'
    #end if
    -match $est.estadvalign.match
    -mismatch $est.estadvalign.mismatch
    -gap $est.estadvalign.gap
    -gap-ext $est.estadvalign.gapext
#else:
    -t $est.redtol
#end if
#if $twod.twod_select == '-2d':
    -i2 '$fasta_in2'
    #if $advanced.advalign.style == 'local':
        -s2 $advanced.advalign.advancedtwod.cutoff_diff_len2
        -S2 $advanced.advalign.advancedtwod.aa_cutoff_diff_len2
    #end if
#end if

-b $advanced.band_width
-l $advanced.throw_away_len
#if $advanced.advalign.style == 'local':
    -G 0
    -aL $advanced.advalign.align_coverage_long
    -AL $advanced.advalign.align_coverage_long_control
    -aS $advanced.advalign.align_coverage_short
    -AS $advanced.advalign.align_coverage_short_control
    -A $advanced.advalign.align_coverage_min
    -s $advanced.advalign.cutoff_diff_len
    -S $advanced.advalign.aa_cutoff_diff_len
#end if
-uL $advanced.max_unmatched_per_l
-uS $advanced.max_unmatched_per_s
-U $advanced.max_unmatched_len
$advanced.accurate
$advanced.inram
$advanced.sort_cluster
$advanced.sort_fasta
#if $print_alnovl.print_alnovl_select == "yes":
    -p 1
    -d $print_alnovl.desclen
#end if

## instead of 800 (default) we use 0:unlimited
-M \${GALAXY_MEMORY_MB:-0}
-T \${GALAXY_SLOTS:-1}