| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/card/rgi/rgi/5.2.1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/card/rgi/rgi/5.1.1 |
| toolshed.g2.bx.psu.edu/repos/card/rgi/rgi/5.1.0 |
| toolshed.g2.bx.psu.edu/repos/card/rgi/rgi/4.2.2 |
| rgi |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| rgi | 5.2.1 | package |
| Additional information about this tool |
#if $db_opts.db_opts_selector == "default":
export DB_PATH='${__tool_data_path__}/rgi_databases/_default' &&
export DATA_PATH="\$_GALAXY_JOB_TMP_DIR" &&
mkdir -p "\$DB_PATH" &&
#end if
#if $db_opts.db_opts_selector != "default":
rgi load
#if $db_opts.db_opts_selector == "local":
-i "${__tool_data_path__}/rgi_databases/$db_opts.rgi_db_local/card.json"
#else:
-i "$db_opts.rgi_db_hist"
#end if
--local
&&
#end if
rgi main
-i '$input_sequence'
-o out
-t $input_type
-a $alignment_tool
-n "\${GALAXY_SLOTS:-1}"
$include_loose
$low_quality
-d $data
#if $db_opts.db_opts_selector != "default":
--local
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_sequence: test1.fasta input_type: contig alignment_tool: blast include_loose: False low_quality: False data: NA db_opts|db_opts_selector: default |
name: value |
test1.fasta value |