Mercurial > repos > iuc > iedb_api
changeset 0:fe3c43451319 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
| author | iuc |
|---|---|
| date | Fri, 28 Feb 2020 18:09:34 -0500 |
| parents | |
| children | 6cf84410cb2e |
| files | iedb_api.py iedb_api.xml static/images/IEDB_Workflow_QueryTabular.png static/images/IEDB_Workflow_TextProcessing.png static/images/IEDB_formatted_alleles.png static/images/TextProcessingConversion.png static/images/seq2HLA_ClassI.HLAgenotype4digits.png test-data/alleles.tsv test-data/bcell.fa test-data/seqs.fa test-data/seqs.tsv |
| diffstat | 11 files changed, 810 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/iedb_api.py Fri Feb 28 18:09:34 2020 -0500 @@ -0,0 +1,319 @@ +#!/usr/bin/env python + +import argparse +import os.path +import re +import sys +import time +from urllib.error import HTTPError +from urllib.parse import unquote, urlencode +from urllib.request import urlopen + +mhci_methods = ['recommended', 'consensus', + 'netmhcpan_ba', 'netmhcpan_el', + 'ann', 'smmpmbec', 'smm', + 'comblib_sidney2008', 'netmhccons', + 'pickpocket', 'netmhcstabpan'] +mhcii_methods = ['recommended', 'consensus', 'NetMHCIIpan', + 'nn_align', 'smm_align', 'comblib', 'tepitope'] +processing_methods = ['recommended', 'netmhcpan', 'ann', + 'smmpmbec', 'smm', 'comblib_sidney2008', + 'netmhccons', 'pickpocket'] +mhcnp_methods = ['mhcnp', 'netmhcpan'] +bcell_methods = ['Bepipred', 'Chou-Fasman', 'Emini', 'Karplus-Schulz', + 'Kolaskar-Tongaonkar', 'Parker', 'Bepipred-2.0'] +prediction_methods = {'mhci': mhci_methods, + 'mhcii': mhcii_methods, + 'processing': processing_methods, + 'mhcnp': mhcnp_methods, + 'bcell': bcell_methods} +all_methods = set(mhci_methods + mhcii_methods + + mhcnp_methods + bcell_methods) +prediction_lengths = {'mhci': range(8, 16), + 'mhcii': range(11, 31), + 'processing': range(8, 15), + 'mhcnp': range(8, 12), + 'bcell': range(8, 16)} + + +def parse_alleles(allelefile, lengths): + alleles = [] + lengths = [] + with open(allelefile, 'r') as fh: + for i, line in enumerate(fh): + fields = line.strip().split(',') + allele = fields[0].strip() + if allele: + if len(fields) > 1: + for alen in fields[1:]: + alleles.append(allele) + lengths.append(alen) + elif lengths: + for alen in str(lengths).split(','): + alleles.append(allele) + lengths.append(alen) + else: + alleles.append(allele) + return (alleles, lengths) + + +def query(url, prediction, seq, allele, length, results, + seqid=None, method='recommended', proteasome=None, + timeout=300, retries=3, sleep=300, debug=False): + params = dict() + if method: + params['method'] = method.encode() + if proteasome: + params['proteasome'] = proteasome.encode() + params['sequence_text'] = seq.strip().encode() + if allele is not None: + params['allele'] = allele.encode() + if length is not None: + if prediction == 'bcell': + params['window_size'] = str(length).encode() + else: + params['length'] = str(length).encode() + req_data = urlencode(params) + if debug: + print('url %s %s' % (url, unquote(req_data)), file=sys.stderr) + retries = max(0, retries) + 1 + for retry in range(1, retries): + response = None + try: + response = urlopen(url, data=req_data.encode('utf-8'), + timeout=timeout) + if response and response.getcode() == 200: + data = [line.decode() for line in response.readlines()] + if debug: + print(data, file=sys.stderr) + rslts = results['prediction']['entries'] + for ln, line in enumerate(data): + if 'invalid' in line.lower() or 'tools_api.html' in line: + msg = '%s %s\n%s' % (url, unquote(req_data), + ''.join(data)) + warn_err(msg, exit_code=1) + if line.find('eptide') > 0: + results['prediction']['header'] = "#%s%s" %\ + ("ID\t" if seqid else "", line) + continue + elif method == 'Bepipred' and line.find('Residue') > 0: + results['detail']['header'] = "#%s%s" %\ + ("ID\t" if seqid else "", line) + rslts = results['detail']['entries'] + continue + if seqid: + rslts.extend("%s\t%s" % (seqid, line)) + else: + rslts.extend(line) + break + else: + code = response.getcode() if response else 1 + warn_err("Error connecting to IEDB server\n", + exit_code=code) + except HTTPError as e: + code = None if retry < retries else e.code + warn_err("%d of %d Error connecting to IEDB server %s\n" % + (retry, retries, e), + exit_code=code) + time.sleep(sleep) + except Exception as e: + warn_err("Error connecting to IEDB server %s\n" % e, + exit_code=3) + return results + + +def warn_err(msg, exit_code=1): + sys.stderr.write(msg) + sys.stderr.flush() + if exit_code: + sys.exit(exit_code) + + +def __main__(): + # Parse Command Line + parser = argparse.ArgumentParser(description='', epilog='') + parser.add_argument('-p', '--prediction', + default='mhci', + choices=prediction_methods.keys(), + help='IEDB API prediction service') + parser.add_argument('-s', '--sequence', + action="append", + default=None, + help='Peptide Sequence') + parser.add_argument('-m', '--method', + default='recommended', + choices=all_methods, + help='prediction method') + parser.add_argument('-P', '--proteasome', + default=None, + choices=['immuno', 'constitutive'], + help='IEDB processing proteasome type') + parser.add_argument('-a', '--allele', + action="append", + default=[], + help='Alleles for which to make predictions') + parser.add_argument('-A', '--allelefile', + default=None, + help='File of HLA alleles') + parser.add_argument('-l', '--length', + action="append", + default=[], + help='lengths for which to make predictions, ' + + '1 per allele') + parser.add_argument('-w', '--window_size', + type=int, + default=None, + help='window_size for bcell prediction') + parser.add_argument('-i', '--input', + default=None, + help='Input file for peptide sequences ' + + '(fasta or tabular)') + parser.add_argument('-c', '--column', + default=None, + help='Peptide Column in a tabular input file') + parser.add_argument('-C', '--id_column', + default=None, + help='ID Column in a tabular input file') + parser.add_argument('-o', '--output', + default=None, + help='Output file for query results') + parser.add_argument('-O', '--output2', + default='iedb_results2', + help='Output file for secondary query results') + parser.add_argument('-t', '--timeout', + type=int, + default=600, + help='Seconds to wait for server response') + parser.add_argument('-r', '--retries', + type=int, + default=5, + help='Number of times to retry server query') + parser.add_argument('-S', '--sleep', + type=int, + default=300, + help='Seconds to wait between retries') + parser.add_argument('-d', '--debug', + action='store_true', + default=False, + help='Turn on wrapper debugging to stderr') + args = parser.parse_args() + + aapat = '^[ABCDEFGHIKLMNPQRSTVWY]+$' + + if args.prediction != 'bcell': + if not args.allele and not args.allelefile: + warn_err('-a allele or -A allelefile required\n', exit_code=1) + + if not (args.sequence or args.input): + warn_err('NO Sequences given: ' + + 'either -s sequence or -i input_file is required\n', + exit_code=1) + + if args.output is not None: + try: + outputPath = os.path.abspath(args.output) + outputFile = open(outputPath, 'w') + except Exception as e: + warn_err("Unable to open output file: %s\n" % e, exit_code=1) + else: + outputFile = sys.stdout + + # params + alleles = [] + lengths = [] + if args.prediction == 'bcell' and args.window_size is not None: + lengths.append(str(args.window_size)) + else: + if args.allelefile: + (alleles, lengths) = parse_alleles(args.allelefile, args.length) + if args.allele: + for i, allele in enumerate(args.allele): + alleles.append(allele) + alen = args.length[i] if i < len(args.length) else args.length[-1] + lengths.append(alen) + allele = ','.join(alleles) if alleles else None + length = ','.join(lengths) if lengths else None + method = args.method + proteasome = args.proteasome if args.prediction == 'processcing' else None + url = 'http://tools-cluster-interface.iedb.org/tools_api/%s/' %\ + args.prediction + + # results + results = {'prediction': {'header': None, 'entries': []}, 'detail': {'header': None, 'entries': []}} + + if args.sequence: + for i, seq in enumerate(args.sequence): + seqid = 'pep_%d' % i + query(url, args.prediction, seq, allele, length, results, + seqid=seqid, method=method, proteasome=proteasome, + timeout=args.timeout, retries=args.retries, + sleep=args.sleep, debug=args.debug) + if args.input: + try: + fh = open(args.input, 'r') + if args.column: # tabular + col = int(args.column) + idcol = int(args.id_column) if args.id_column else None + for i, line in enumerate(fh): + fields = line.rstrip('\r\n').split('\t') + if len(fields) > col: + seq = re.sub('[_*]', '', fields[col].strip()) + if re.match(aapat, seq): + if idcol is not None and idcol < len(fields): + seqid = fields[idcol] + else: + seqid = 'pep_%d' % i + query(url, args.prediction, seq, allele, length, + results, seqid=seqid, + method=method, proteasome=proteasome, + timeout=args.timeout, retries=args.retries, + sleep=args.sleep, debug=args.debug) + else: + warn_err('Line %d, Not a peptide: %s\n' % (i, seq), + exit_code=None) + else: # fasta + seqid = None + seq = '' + for i, line in enumerate(fh): + if line.startswith('>'): + if seqid and len(seq) > 0: + query(url, args.prediction, seq, allele, length, + results, seqid=seqid, + method=method, proteasome=proteasome, + timeout=args.timeout, retries=args.retries, + sleep=args.sleep, debug=args.debug) + seqid = line[1:].strip() + seq = '' + else: + seq += line.strip() + if seqid and len(seq) > 0: + query(url, args.prediction, seq, allele, length, + results, seqid=seqid, + method=method, proteasome=proteasome, + timeout=args.timeout, retries=args.retries, + sleep=args.sleep, debug=args.debug) + fh.close() + except Exception as e: + warn_err("Unable to open input file: %s\n" % e, exit_code=1) + + if results['prediction']['header']: + outputFile.write(results['prediction']['header']) + for line in results['prediction']['entries']: + outputFile.write(line) + if results['detail']['entries']: + if args.output2: + try: + outPath = os.path.abspath(args.output2) + outFile = open(outPath, 'w') + except Exception as e: + warn_err("Unable to open output file: %s\n" % e, exit_code=1) + else: + outFile = sys.stdout + if results['detail']['header']: + outFile.write(results['detail']['header']) + for line in results['detail']['entries']: + outFile.write(line) + + +if __name__ == "__main__": + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/iedb_api.xml Fri Feb 28 18:09:34 2020 -0500 @@ -0,0 +1,477 @@ +<tool id="iedb_api" name="IEDB" version="2.15.0"> + <description>MHC Binding prediction</description> + <macros> + <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples=""> + <conditional name="alleles"> + <param name="allelesrc" type="select" label="Alleles"> + <option value="history">From history</option> + <option value="entry">Entered</option> + </param> + <when value="history"> + <param name="allele_file" type="data" format="txt" label="Alleles file"> + <help>The dataset should have on allele per line. The allele may be followed by an optional comma-separated list of peptide lengths, e.g.: @HLALEN_EXAMPLES@</help> + </param> + </when> + <when value="entry"> + <param name="allele_text" type="text" size="80" label="Alleles"> + <help>Enter alleles separated by white space: @HLA_EXAMPLES@ (The peptide lengths may follow each allele: @HLALEN_EXAMPLES@)</help> + <validator type="regex" message="Doesn't appear to be a valid allele">^@HLA_REGEX@(\s+@HLA_REGEX@)*$</validator> + </param> + </when> + </conditional> + </xml> + </macros> + <requirements> + <requirement type="package" version="3.7">python</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ + #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 + #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' + ]]></command> + <configfiles> + <configfile name="entered_alleles"><![CDATA[#slurp +#if $prediction.tool != 'bcell' and $prediction.alleles.allelesrc == 'entry' +#for $word in str($prediction.alleles.allele_text).strip().split(): +#if $word.find(',') > 0 +$word +#else +#set $allele = $word + ',' + str($prediction.lengths) +$allele +#end if +#end for +#end if +]]></configfile> + <configfile name="entered_seqs"><![CDATA[#slurp +#if $sequence.seqsrc == 'entry' +#for $i, $seq in enumerate(str($sequence.seq_text).strip().split()) +#set $seqid = $i + 1 +#set $seqtext = '\t'.join([str($seqid),$seq.strip()]) +$seqtext +#end for +#end if +]]></configfile> + </configfiles> + <inputs> + <conditional name="prediction"> + <param name="tool" type="select" label="Prediction"> + <option value="mhci">MHC-I Binding</option> + <option value="mhcii">MHC-II Binding</option> + <option value="processing">MHC-I Processing</option> + <option value="mhcnp">MHC-NP T-Cell Epitope</option> + <option value="bcell">Antibody Epitope Prediction</option> + </param> + <when value="mhci"> + <param name="method" type="select" label="prediction method"> + <option value="recommended" selected="true">recommended</option> + <option value="consensus">consensus</option> + <option value="netmhcpan">netmhcpan</option> + <option value="ann">ann</option> + <option value="smmpmbec">smmpmbec</option> + <option value="smm">smm</option> + <option value="comblib_sidney2008">comblib_sidney2008</option> + <option value="netmhccons">netmhccons</option> + <option value="pickpocket">pickpocket</option> + </param> + <expand macro="alleles" hla_regex="(HLA-[A-CEG]\*[0-8][[0-9]:[0-9][0-9][0-9]*|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-5]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/> + <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> + <help>Used for any alleles which don't include specified lengths</help> + <option value="8" selected="true">8</option> + <option value="9">9</option> + <option value="10">10</option> + <option value="11">11</option> + <option value="12">12</option> + <option value="13">13</option> + <option value="14">14</option> + <option value="15">15</option> + </param> + + </when> + <when value="mhcii"> + <param name="method" type="select" label="prediction method"> + <option value="recommended" selected="true">recommended</option> + <option value="consensus3">consensus3</option> + <option value="NetMHCIIpan">NetMHCIIpan</option> + <option value="nn_align">nn_align</option> + <option value="smm_align">smm_align</option> + <option value="comblib">comblib</option> + <option value="tepitope">tepitope</option> + </param> + <expand macro="alleles" hla_regex="(DPA1\*0[1-3](:0[1-3])?/DPB1\*0[1-6]:0[12]|DQA1\*0[1-5]:0[12]/DQB1\*0[2-6]:0[12]|(HLA-)?DRB[1-5]\*[01][1-9]:0[1-5]|H2-IA[bd])(,(asis|[1-2][0-9]|30))*" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb" hlalen_examples="DPA1*01/DPB1*04:01,11,15"/> + <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> + <help>Used for any alleles which don't include specified lengths</help> + <option value="asis">asis</option> + <option value="11">11</option> + <option value="12">12</option> + <option value="13">13</option> + <option value="14">14</option> + <option value="15" selected="true">15</option> + <option value="16">16</option> + <option value="17">17</option> + <option value="18">18</option> + <option value="19">19</option> + <option value="20">20</option> + <option value="21">21</option> + <option value="22">22</option> + <option value="23">23</option> + <option value="24">24</option> + <option value="25">25</option> + <option value="26">26</option> + <option value="27">27</option> + <option value="28">28</option> + <option value="29">29</option> + <option value="30">30</option> + </param> + </when> + <when value="processing"> + <param name="method" type="select" label="prediction method"> + <option value="recommended" selected="true">recommended</option> + <option value="consensus">consensus</option> + <option value="netmhcpan">netmhcpan</option> + <option value="ann">ann</option> + <option value="smmpmbec">smmpmbec</option> + <option value="smm">smm</option> + <option value="comblib_sidney2008">comblib_sidney2008</option> + </param> + <param name="proteasome" type="select" label="proteasome type"> + <option value="immuno">immuno</option> + <option value="constitutive">constitutive</option> + </param> + <expand macro="alleles" hla_regex="(HLA-[A-CE]\*[0-8][[0-9]:[0-9][0-9]|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-4]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/> + <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> + <help>Used for any alleles which don't include specified lengths</help> + <option value="8" selected="true">8</option> + <option value="9">9</option> + <option value="10">10</option> + <option value="11">11</option> + <option value="12">12</option> + <option value="13">13</option> + <option value="14">14</option> + </param> + </when> + <when value="mhcnp"> + <param name="method" type="select" label="prediction method"> + <option value="mhcnp" selected="true">mhcnp</option> + <option value="netmhcpan">netmhcpan</option> + </param> + <expand macro="alleles" hla_regex="(HLA-(A\*02:01|B\*07:02|B\*35:01|B\*44:03|B\*53:01|B\*57:01)|H-2-[DK]b)(,[8-9]|1[0-1])*" hla_examples="HLA-A*02:01 H-2-Db" hlalen_examples="HLA-A*02:01,8,9,10"/> + <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> + <help>Used for any alleles which don't include specified lengths</help> + <option value="8" selected="true">8</option> + <option value="9">9</option> + <option value="10">10</option> + <option value="11">11</option> + </param> + </when> + <when value="bcell"> + <param name="method" type="select" label="prediction method"> + <option value="Bepipred" selected="true">Bepipred</option> + <option value="Chou-Fasman">Chou-Fasman</option> + <option value="Emini">Emini</option> + <option value="Karplus-Schulz">Karplus-Schulz</option> + <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option> + <option value="Parker">Parker</option> + </param> + <param name="window_size" type="integer" value="" optional="true" min="1" label="window_size" help="window_size should be less than the sequence length, and less than 8 for Karplus-Schulz method"/> + </when> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" type="select" label="Peptide sequences"> + <option value="fasta">Fasta file</option> + <option value="tabular">From tabular</option> + <option value="entry"></option> + </param> + <when value="fasta"> + <param name="seq_fasta" type="data" format="fasta" label="Peptide Sequence Fasta"/> + </when> + <when value="tabular"> + <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/> + <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" /> + <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/> + </when> + <when value="entry"> + <param name="seq_text" type="text" label="Peptide Sequence"/> + </when> + </conditional> + + </inputs> + <outputs> + <!-- + <data name="output" format="tabular"/> + --> + <data name="output" format="tabular" label="IEDB ${prediction.tool} ${prediction.method}"/> + <data name="output2" format="tabular" label="IEDB ${prediction.tool} ${prediction.method} residue scores" from_work_dir="iedb_results2"> + <filter>prediction['method'].startswith('Bepipred')</filter> + </data> + </outputs> + <tests> + <!-- test1 --> + <test> + <conditional name="prediction"> + <param name="tool" value="mhci"/> + <param name="method" value="recommended"/> + <conditional name="alleles"> + <param name="allelesrc" value="entry"/> + <param name="allele_text" value="HLA-A*01:01,9"/> + </conditional> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="entry"/> + <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="LYNTVATLY" /> + </assert_contents> + </output> + </test> + <!-- test2 --> + <test> + <conditional name="prediction"> + <param name="tool" value="mhci"/> + <param name="method" value="recommended"/> + <conditional name="alleles"> + <param name="allelesrc" value="history"/> + <param name="allele_file" ftype="tabular" value="alleles.tsv"/> + </conditional> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="fasta"/> + <param name="seq_fasta" ftype="fasta" value="seqs.fa"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="peptide1" /> + <has_text text="HKVPRRLLK" /> + </assert_contents> + </output> + </test> + <!-- test3 --> + <test> + <conditional name="prediction"> + <param name="tool" value="mhci"/> + <param name="method" value="recommended"/> + <conditional name="alleles"> + <param name="allelesrc" value="history"/> + <param name="allele_file" ftype="tabular" value="alleles.tsv"/> + </conditional> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="tabular"/> + <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/> + <param name="pep_col" value="3"/> + <param name="id_col" value="1"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="peptide1" /> + <has_text text="HKVPRRLLK" /> + </assert_contents> + </output> + </test> + <!-- test4 --> + <test> + <conditional name="prediction"> + <param name="tool" value="mhcii"/> + <param name="method" value="recommended"/> + <conditional name="alleles"> + <param name="allelesrc" value="entry"/> + <param name="allele_text" value="DPA1*01/DPB1*04:01"/> + </conditional> + <param name="lengths" value="asis"/> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="entry"/> + <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="LYNTVATLY" /> + </assert_contents> + </output> + </test> + <!-- test5 --> + <test> + <conditional name="prediction"> + <param name="tool" value="processing"/> + <param name="method" value="recommended"/> + <conditional name="alleles"> + <param name="allelesrc" value="entry"/> + <param name="allele_text" value="HLA-A*01:01,8 HLA-A*02:01,9"/> + </conditional> + <param name="proteasome" value="constitutive"/> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="entry"/> + <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="LYNTVATLY" /> + </assert_contents> + </output> + </test> + <!-- test6 --> + <test> + <conditional name="prediction"> + <param name="tool" value="mhcnp"/> + <param name="method" value="mhcnp"/> + <conditional name="alleles"> + <param name="allelesrc" value="entry"/> + <param name="allele_text" value="HLA-A*02:01,9"/> + </conditional> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="entry"/> + <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="LYNTVATLY" /> + </assert_contents> + </output> + </test> + <!-- test7 --> + <test> + <conditional name="prediction"> + <param name="tool" value="bcell"/> + <param name="method" value="Emini"/> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="entry"/> + <param name="seq_text" value="VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTE"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="VLSEGE" /> + </assert_contents> + </output> + </test> + <!-- test8 --> + <test> + <conditional name="prediction"> + <param name="tool" value="bcell"/> + <param name="method" value="Bepipred"/> + <param name="window_size" value="9"/> + </conditional> + <conditional name="sequence"> + <param name="seqsrc" value="fasta"/> + <param name="seq_fasta" ftype="fasta" value="bcell.fa"/> + </conditional> + <output name="output"> + <assert_contents> + <has_text text="ADVAGH" /> + </assert_contents> + </output> + </test> + + </tests> + <help><![CDATA[ +The IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases. It offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species. + +This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB. +The webservices are described at: http://tools.immuneepitope.org/main/tools-api/ +That page also describes how to retrieve the available HLA alleles for class of epitope binding. + +**INPUTS** + + peptide sequences from a fasta file or a column in a tabular file + + HLA alleles either entered as text or one per line in a text file + + +**OUTPUTS** + + A tabular file containing the results returned from the IEDB web service + +**Typical Workflow for Human MHC I Binding Prediction** + +The RNAseq data for the subject would be used for: + + - HLA prediction by seq2HLA + - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta + + +.. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png + :width: 584 + :height: 430 + +.. note:: The seq2HLA ClassI.HLAgenotype4digits output needs to be converted for IEDB alleles. + +The seq2HLA ClassI.HLAgenotype4digits output: + +.. image:: $PATH_TO_IMAGES/seq2HLA_ClassI.HLAgenotype4digits.png + :width: 285 + :height: 77 + +Needs to be converted into IEDB formatted alleles: + +.. image:: $PATH_TO_IMAGES/IEDB_formatted_alleles.png + :width: 74 + :height: 81 + +In the workflow above QueryTabular tool converts the alleles: + + - Filter Dataset Input + + * skip leading lines - *skip lines:* 1 + * select columns - *columns:* 2,4 + * regex replace value in column - *column:* 1 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1 + * regex replace value in column - *column:* 2 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1 + + - SQL Query to generate tabular output + + * SELECT c1 FROM t1 UNION SELECT c2 FROM t1 + + +The IEDB formatting can also be performed by TextProcessing tools: + +.. image:: $PATH_TO_IMAGES/TextProcessingConversion.png + :width: 608 + :height: 87 + +The TextProcessing steps to convert the alleles: + + - Remove beginning - removes the header line + - Replace Text - picks Allele 1 and Allele 2 from each line and reformats each on a separate line + + * *Find pattern:* ^.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*$ + * *Replace with:* HLA-\\1\\nHLA-\\2 + + - Unique - remove duplicates + + + ]]></help> + <citations> + <citation type="doi">10.1093/nar/gku938</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alleles.tsv Fri Feb 28 18:09:34 2020 -0500 @@ -0,0 +1,2 @@ +HLA-A*01:01,9 +HLA-A*03:01,10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bcell.fa Fri Feb 28 18:09:34 2020 -0500 @@ -0,0 +1,6 @@ +>pep1 +VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTE +>pep2 +AGHAHKVPRRLLKAAR +>pep3 +ALKAADASADADGSGSGSGSGAGHAHKVPRRLLKAAR