| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/thanhlv/socru/socru/2.2.4 (this tool) |
| toolshed.g2.bx.psu.edu/repos/thanhlv/socru/socru/2.2.2 |
| toolshed.g2.bx.psu.edu/repos/thanhlv/socru/socru/2.2.1 |
| toolshed.g2.bx.psu.edu/repos/thanhlv/socru/socru/2.1.7 |
| toolshed.g2.bx.psu.edu/repos/thanhlv/socru/socru/2.1.4 |
| toolshed.g2.bx.psu.edu/repos/thanhlv/socru/socru/2.1.2 |
| toolshed.g2.bx.psu.edu/repos/thanhlv/socru/socru/2.1.0 |
| toolshed.g2.bx.psu.edu/repos/thanhlv/socru/socru/1.0.1 |
| toolshed.g2.bx.psu.edu/repos/thanhlv/socru/socru/1.0.0 |
| toolshed.g2.bx.psu.edu/repos/thanhlv/socru/socru/0.0.5 |
| socru |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| socru | 2.2.4 | package |
| Additional information about this tool |
#import re
#import os.path
#set $_input_file = re.sub(r'(\s|\(|\)|:|!)', '_', str($assembly.element_identifier))
ln -s '${assembly}' $_input_file &&
socru
--threads \${GALAXY_SLOTS:-4}
--top_blast_hits top_blast_hits.tsv
#if str($opt_args.max_bases_from_ends) != ""
--max_bases_from_ends $opt_args.max_bases_from_ends
#end if
#if $opt_args.not_circular
$opt_args.not_circular
#end if
--min_bit_score $opt_args.min_bit_score
--min_alignment_length $opt_args.min_alignment_length
#if $opt_args.verbose
$opt_args.verbose
#end if
$species ${_input_file}
> $output
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
assembly: test.fa species: Salmonella_enterica |
name: value |
test.fa value |