#set $inputs = ""
#for i, f in enumerate($input):
    #set $inputs = $inputs + " input" + str($i) + ".gbk"
    ln -s '$f' input${i}.gbk &&
#end for

funannotate compare
--input

$inputs

--out output

--database '$database.fields.path'

#if $run_dnds in ['estimate', 'full']:
    --run_dnds ${run_dnds}
#end if

## need to add --outgroup option some day (hard to get an up to date/customizable list)

--go_fdr ${go_fdr}

--heatmap_stdev ${heatmap_stdev}

--num_orthos ${num_orthos}

#if $proteinortho:
    --proteinortho '${proteinortho}'
#end if

--ml_method ${ml.ml_method}

#if $ml.ml_method == 'raxml':
    --bootstrap '${ml.bootstrap}'
#end if

--cpus \${GALAXY_SLOTS:-2}

&&

mkdir -p '$output.files_path' &&
cp -R output/* '$output.files_path' &&
cp output/index.html '$output'