| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.13.0+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.13.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.13.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.13.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.12.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.10.2 |
| toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/0.1.0 |
| roary |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| roary | 3.13.0 | package |
| Additional information about this tool |
#import re
#set $filenames = list()
## Roary resolves symbolic links and breaks if there is whitespace in the path.
## Copying and renaming the files resolves that issue.
#for $gff in $gff_input.gffs
#set $filename = '%s.gff' % re.sub('[^\w_-]', '_', str($gff.element_identifier))
cp '$gff' $filename &&
$filenames.append(str($filename))
#end for
roary
-f out
-p \${GALAXY_SLOTS:-1}
-e
-n
-i '$percent_ident'
-cd '$core_diff'
-g '$advanced.maxclust'
$advanced.split_para
-t '$advanced.trans_tab'
-iv '$advanced.mcl'
#for $f in $filenames
'$f'
#end for
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
gff_input|gffs: ['ex1.gff', 'ex2.gff'] gff_input|gff_input_selector: individual |
name: value |
ex1.gff ex2.gff value |
| Test-2 |
gff_input|gffs: ['ex1.gff', 'ex2.gff'] gff_input|gff_input_selector: individual percent_ident: 50 core_diff: 50.0 |
name: value |
ex1.gff ex2.gff value |