| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.3.6+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.3.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.3.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.3.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.3.1+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.2.3+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.2.3+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.1.2+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.32+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.31+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.31+galaxy0 |
| proteinortho_grab_proteins |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| proteinortho | 6.3.6 | package |
| diamond | 2.1.12 | package |
| blast | 2.16.0 | package |
| ucsc-blat | 481 | package |
| last | 1639 | package |
| mmseqs2 | 17.b804f | package |
| Additional information about this tool |
## the following ln-action is necessary, since the file names are used by proteinortho (output contains filenames => species names)
#import re
#for $f in $input_files#
ln -sf '$f' '${re.sub('[^\w\-_.]', '_', f.element_identifier)}' &&
#end for#
#if $query.querytype == "file":
ln -sf '$query.queryfile' 'query' &&
#end if
mkdir output && cd output &&
proteinortho_grab_proteins.pl
--tofiles
$regex
$source
#if $query.querytype == "string":
'$query.querystring'
#else:
../query
#end if
#for $f in $input_files#
../${re.sub('[^\w\-_.]', '_', f.element_identifier)}
#end for#
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_files: ['L.fasta', 'C.fasta', 'C2.fasta', 'E.fasta', 'M.fasta'] query|querystring: E_1 query|querytype: string |
L.fasta C.fasta C2.fasta E.fasta M.fasta |
|
| Test-2 |
input_files: ['L.fasta', 'C.fasta', 'C2.fasta', 'E.fasta', 'M.fasta'] query|querystring: M..2 query|querytype: string regex: True source: True |
L.fasta C.fasta C2.fasta E.fasta M.fasta |
|
| Test-3 |
input_files: ['L.fasta', 'C.fasta', 'C2.fasta', 'E.fasta', 'M.fasta'] query|queryfile: result.proteinortho.tsv query|querytype: file |
L.fasta C.fasta C2.fasta E.fasta M.fasta result.proteinortho.tsv |