Repository revision
4:7ed6dda64a81

Repository 'iedb_api'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/iedb_api

IEDB tool metadata
Miscellaneous
IEDB
MHC Binding prediction
iedb_api
toolshed.g2.bx.psu.edu/repos/iuc/iedb_api/iedb_api/2.15.2
2.15.2
None
True
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'
    
None
False
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