set -o pipefail; export TERM=vt100; 

#import re

#set fastas = ''
#set groups = ''
#set count = 0

#if $method.how == 'collection':
    #for $i in $method.fasta_collection:
        #set $identifier=re.sub('[^\w_]', '_', str($i.element_identifier))
        ln -s '$i' 'fasta_${identifier}.dat' &&
        #set fastas+='fasta_'+$identifier+'.dat-'
        #set groups+=$identifier+'-'
    #end for
#else
    #for $i in $method.inputs:
        ln -s '$i.fasta' fasta_${count}.dat &&
        #set fastas+='fasta_'+str($count)+'.dat-'
        #set groups+=str($i.group)+'-'
        #set count+=1
    #end for
#end if

echo 'make.group(
    fasta=${ str($fastas).rstrip('-') },
    groups=${ str($groups).rstrip('-') }
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log