# HG changeset patch
# User iuc
# Date 1582931374 18000
# Node ID fe3c434513196df56dae013bb3c75310b9f2f710

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"

diff -r 000000000000 -r fe3c43451319 iedb_api.py
--- /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__()
diff -r 000000000000 -r fe3c43451319 iedb_api.xml
--- /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>
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diff -r 000000000000 -r fe3c43451319 static/images/IEDB_Workflow_TextProcessing.png
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diff -r 000000000000 -r fe3c43451319 static/images/IEDB_formatted_alleles.png
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diff -r 000000000000 -r fe3c43451319 static/images/TextProcessingConversion.png
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diff -r 000000000000 -r fe3c43451319 static/images/seq2HLA_ClassI.HLAgenotype4digits.png
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diff -r 000000000000 -r fe3c43451319 test-data/alleles.tsv
--- /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
diff -r 000000000000 -r fe3c43451319 test-data/bcell.fa
--- /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
diff -r 000000000000 -r fe3c43451319 test-data/seqs.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqs.fa	Fri Feb 28 18:09:34 2020 -0500
@@ -0,0 +1,4 @@
+>peptide1
+GHAHKVPRRLLKAAR
+>peptide2
+LKAADASADADGSGSGSGSG
diff -r 000000000000 -r fe3c43451319 test-data/seqs.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqs.tsv	Fri Feb 28 18:09:34 2020 -0500
@@ -0,0 +1,2 @@
+peptide1	16	GHAHKVPRRLLKAAR
+peptide2	21	LKAADASADADGSGSGSGSG