## Needed by some subprocess invoked internally
## https://github.com/nextgenusfs/funannotate/issues/905
export FUNANNOTATE_DB='$database.fields.path' &&

## show detailed info about the reference DB on stdout
funannotate database &&

funannotate annotate

#if $input.input_type == 'gbk'
    --genbank '${input.genbank}'
#else
    --gff '${input.gff}'
    --fasta '${input.fasta}'
    --species '${input.species}'
#end if

--out output
--tmpdir "\${_GALAXY_JOB_TMP_DIR:-/tmp}"

--database '$database.fields.path'

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

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

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

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

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

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

--busco_db '${busco_db}'

--isolate '${isolate}'
--strain '${strain}'

#if $rename:
    --rename '${rename}'
#end if
#if $fix:
    --fix '${fix}'
#end if
#if $remove:
    --remove '${remove}'
#end if
--header_length $header_length
--cpus \${GALAXY_SLOTS:-2}

&&

## Funannotate sometimes leaves multiple *part.tbl and *part.sqn files:
## https://github.com/nextgenusfs/funannotate/issues/777
## The partial tbl files are combined by funannotate and are deleted below.
## The sqn files are discrete and are collected with discover_datasets.
find output/annotate_results
-regex ".*part_[0-9]+\.\(tbl\)$"
-delete