#set $inputs = []
#set $input_compression = []
#for r in $input.selection:
    #if $input.type == "protein":
        #silent $inputs.append($r.input_file)
        #silent $input_compression.append($r.input_file.is_of_type('fasta.gz'))
    #elif $r.nuc_choice.source == "history":
        #silent $inputs.append($r.nuc_choice.input_file)
        #silent $input_compression.append($r.nuc_choice.input_file.is_of_type('fasta.gz'))
    #else:
        #silent $inputs.append($r.nuc_choice.input_file.fields.path)
        #silent $input_compression.append(False)
    #end if
#end for

python $__tool_directory__/check_no_duplicates.py
##First check for duplicates (since BLAST+ 2.2.28 fails to do so)
##and abort (via the ampersand ampersand trick) if any are found.
#for i in $inputs#'$i' #end for#
&&
##makeblastdb does not like input redirects of the sort
##makeblastdb -in <(gunzip -c gzipped_fasta_file)
##therefore we're cramming everything
##into a single cat command below
cat
#for i, is_gzipped in zip($inputs, $input_compression):
    #if $is_gzipped:
        <(gunzip -c '$i')
    #else:
        '$i'
    #end if
#end for
| makeblastdb -out '${os.path.join($outfile.files_path, "blastdb")}'
-blastdb_version 4
$parse_seqids
$hash_index
-in -
#if $title:
-title '${title}'
#else:
##Would default to being based on the cryptic Galaxy filenames, which is unhelpful
-title 'BLAST Database'
#end if
-dbtype
#if $input.type == "protein":
    prot
#else:
    nucl
#end if
## --------------------------------------------------------------------
## Masking
## --------------------------------------------------------------------
## HACK: If no mask files, evaluates as a list with just None in it:
## See Trello issue https://trello.com/c/lp5YmA1O
#if ' '.join( map(str, $mask_data_file) ) != 'None':
#for i in $mask_data_file:
-mask_data '${i}'
#end for
#end if
## --------------------------------------------------------------------
## Taxonomy
## --------------------------------------------------------------------
#if $tax.taxselect == 'id':
-taxid $tax.taxid
## #else if $tax.taxselect == 'map':
## -taxid_map $tax.taxmap
#end if
## --------------------------------------------------------------------
## Capture the stdout log information to the primary file (plain text):
> '$outfile'