set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
ln -s '$tree' tree.dat &&
ln -s '$group' group.dat &&
ln -s '$name' name.dat &&
ln -s '$count' count.dat &&

echo 'unifrac.weighted(
    tree=tree.dat,
    #if $group:
        group=group.dat,
        #if $groups:
            groups=${ str($groups).replace(",","-") },
        #end if
    #end if
    #if $name:
        name=name.dat,
    #end if
    iters=$iters,
    #if $subsampling.use == "yes":
        #if $subsampling.subsample:
            subsample=$subsampling.subsample,
        #else
            subsample=T,
        #end if
        consensus=$subsampling.consensus,
    #else
        random=$random,
    #end if
    #if $distance:
        distance=$distance,
    #end if
    #if $count:
        count=count.dat,
    #end if
    root=$root,
    processors='\${GALAXY_SLOTS:-1}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log

## rename some datasets
#if $subsampling.use == "yes":
    && mv tree.*.ave.dist tree.ave
    && mv tree.*.std.dist tree.std
#end if