set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
ln -s '$input.otu' input_otu.dat &&
ln -s '$count' count.dat &&
ln -s '$taxonomy' taxonomy.dat &&
#if $input.format == "fasta":
    ln -s '$input.name_in' input_name_in.dat &&
#end if
#if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes":
    ln -s '$input.use_group.group_in' input_use_group_group_in.dat &&
#end if

echo 'sub.sample(
    #if $input.format == "fasta":
        fasta=input_otu.dat
        #if $input.name_in:
            ,name=input_name_in.dat
        #end if
    #else
        #if $input.format == "list":
            list=input_otu.dat
        #elif $input.format == "sabund":
            sabund=input_otu.dat
        #elif $input.format == "rabund":
            rabund=input_otu.dat
        #elif $input.format == "shared":
            shared=input_otu.dat
            #if $input.groups:
                ,groups=${ str($input.groups).replace(",","-") }
            #end if
        #end if
        #if $input.label:
            ,label=${ str($input.label).replace(",","-") }
        #end if
    #end if
    #if $input.format == "fasta" or $input.format == "list":
        #if $input.use_group.to_filter == "yes":
            ,group=input_use_group_group_in.dat
            #if $input.use_group.groups:
                ,groups=${ str($input.use_group.groups).replace(",","-") }
            #end if
            ,persample=$input.use_group.persample
        #end if
    #end if
    #if $count:
        ,count=count.dat
    #end if
    #if $taxonomy:
        ,taxonomy=taxonomy.dat
    #end if
    #if $size:
        ,size=$size
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log