Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/iedb_api/iedb_api/2.15.2 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/iedb_api/iedb_api/2.15.1 |
toolshed.g2.bx.psu.edu/repos/iuc/iedb_api/iedb_api/2.15.0 |
iedb_api |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
python | 3.7 | package |
Additional information about this tool |
#import re python '${__tool_directory__}/iedb_api.py' --prediction=$prediction.tool --method=$prediction.method #if $prediction.tool == 'bcell': #if $prediction.window_size: -w $prediction.window_size #end if #else #if $prediction.tool == 'processing' and $prediction.proteasome: --proteasome $prediction.proteasome #end if #if $prediction.alleles.allelesrc == 'history': -A '$prediction.alleles.allele_file' #else: -A '$entered_alleles' #end if -l '$prediction.lengths' #end if #if $sequence.seqsrc == 'fasta': -i '$sequence.seq_fasta' #else if $sequence.seqsrc == 'tabular': -i '$sequence.seq_tsv' -c #echo int(str($sequence.pep_col)) - 1 #if $sequence.id_col: -C #echo int(str($sequence.id_col)) - 1 #end if #else: -i '$entered_seqs' -c 1 -C 0 #end if -o '$output'
Functional tests |
name | inputs | outputs | required files |
Test-1 |
prediction|method: recommended prediction|alleles|allele_text: HLA-A*01:01,9 prediction|alleles|allelesrc: entry prediction|tool: mhci sequence|seq_text: SLYNTVATLYCVHQRIDV sequence|seqsrc: entry |
name: value |
value |
Test-2 |
prediction|method: recommended prediction|alleles|allele_file: alleles_len.tsv prediction|alleles|allelesrc: history prediction|tool: mhci sequence|seq_fasta: seqs.fa sequence|seqsrc: fasta |
name: value |
alleles_len.tsv seqs.fa value |
Test-3 |
prediction|method: recommended prediction|alleles|allele_file: alleles.tsv prediction|alleles|allelesrc: history prediction|lengths: ['8', '9'] prediction|tool: mhci sequence|seq_tsv: seqs.tsv sequence|pep_col: 3 sequence|id_col: 1 sequence|seqsrc: tabular |
name: value |
alleles.tsv seqs.tsv value |
Test-4 |
prediction|method: recommended prediction|alleles|allele_text: DPA1*01/DPB1*04:01 prediction|alleles|allelesrc: entry prediction|lengths: asis prediction|tool: mhcii sequence|seq_text: SLYNTVATLYCVHQRIDV sequence|seqsrc: entry |
name: value |
value |
Test-5 |
prediction|method: recommended prediction|proteasome: constitutive prediction|alleles|allele_text: HLA-A*01:01,8 HLA-A*02:01,9 prediction|alleles|allelesrc: entry prediction|tool: processing sequence|seq_text: SLYNTVATLYCVHQRIDV sequence|seqsrc: entry |
name: value |
value |
Test-6 |
prediction|method: mhcnp prediction|alleles|allele_text: HLA-A*02:01,9 prediction|alleles|allelesrc: entry prediction|tool: mhcnp sequence|seq_text: SLYNTVATLYCVHQRIDV sequence|seqsrc: entry |
name: value |
value |
Test-7 |
prediction|method: Emini prediction|tool: bcell sequence|seq_text: VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTE sequence|seqsrc: entry |
name: value |
value |
Test-8 |
prediction|method: Kolaskar-Tongaonkar prediction|window_size: 9 prediction|tool: bcell sequence|seq_fasta: bcell.fa sequence|seqsrc: fasta |
name: value |
bcell.fa value |