##Unlike makeblastdb, makeprofiledb needs directory to exist already:
mkdir -p $outfile.files_path &&
makeprofiledb
-blastdb_version 4
-out '${os.path.join($outfile.files_path, "blastdb")}'

##We turn $input_file into $infiles with a configfile entry defined below
-in '$infiles'

#if $title:
-title '$title'
#else:
##Would default to being based on the cryptic Galaxy filenames, which is unhelpful
-title 'Profile Database'
#end if

-threshold $threshold

#if str($contain_pssm_scores.contain_pssm_scores_type) == 'no':
    -gapopen $contain_pssm_scores.gapopen
    -gapextend $contain_pssm_scores.gapextend
    -scale $contain_pssm_scores.scale
    -matrix $contain_pssm_scores.matrix
#end if

-obsr_threshold $obsr_threshold
-exclude_invalid $exclude_invalid

-logfile '$outfile'