Repository revision
6:64e67f172188

Repository 'get_orfs_or_cdss'
hg clone https://toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss

Get open reading frames (ORFs) or coding sequences (CDSs) tool metadata
Miscellaneous
e.g. to get peptides from ESTs
get_orfs_or_cdss
toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5
0.0.5
python /var/opt/galaxy/g2cmnty/galaxy_toolshed/database/community_files/000/repo_132/tools/get_orfs_or_cdss/get_orfs_or_cdss.py --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.1.1
toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5 (this tool)
toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.3
toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.2
toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.1
get_orfs_or_cdss
Requirements (dependencies defined in the <requirements> tag set)
name version type
biopython 1.62 package
Bio not provided python-module
Functional tests
name inputs outputs required files
Test-1 input_file: get_orf_input.fasta
table: 1
ftype: CDS
ends: open
mode: all
min_len: 10
strand: forward
out_nuc_file: get_orf_input.t1_nuc_out.fasta
out_prot_file: get_orf_input.t1_prot_out.fasta
get_orf_input.fasta
get_orf_input.t1_nuc_out.fasta
get_orf_input.t1_prot_out.fasta
Test-2 input_file: get_orf_input.fasta
table: 11
ftype: CDS
ends: closed
mode: all
min_len: 10
strand: forward
out_nuc_file: get_orf_input.t11_nuc_out.fasta
out_prot_file: get_orf_input.t11_prot_out.fasta
get_orf_input.fasta
get_orf_input.t11_nuc_out.fasta
get_orf_input.t11_prot_out.fasta
Test-3 input_file: get_orf_input.fasta
table: 11
ftype: CDS
ends: open
mode: all
min_len: 10
strand: forward
out_nuc_file: get_orf_input.t11_open_nuc_out.fasta
out_prot_file: get_orf_input.t11_open_prot_out.fasta
get_orf_input.fasta
get_orf_input.t11_open_nuc_out.fasta
get_orf_input.t11_open_prot_out.fasta
Test-4 input_file: Ssuis.fasta
table: 11
ftype: ORF
ends: open
mode: all
min_len: 100
strand: both
out_nuc_file: get_orf_input.Suis_ORF.nuc.fasta
out_prot_file: get_orf_input.Suis_ORF.prot.fasta
Ssuis.fasta
get_orf_input.Suis_ORF.nuc.fasta
get_orf_input.Suis_ORF.prot.fasta