set -o pipefail; export TERM=vt100; 
#import re

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
#for $i in $inputs:
    ln -s '$i.fasta' fasta${inputs.index($i)}.dat &&
#end for
ln -s '$hard' hard.dat &&

echo 'filter.seqs(
    fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#,
    vertical=$vertical,
    #if $trump:
        trump=$trump,
    #end if
    soft=$soft,
    #if $hard:
        hard=hard.dat,
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log &&

## rename collection files for more transparent element naming
#set $identifier=re.sub('[^\w\-\s\.]', '_', str($fasta.element_identifier))
mv fasta.filter.fasta '${identifier}.filter.fasta'
#for i in $inputs:
    #set $identifier=re.sub('[^\w\-\s]', '_', str($i.fasta.element_identifier))
    && mv fasta${inputs.index($i)}.filter.fasta '${identifier}.filter.fasta'
#end for