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comparison iedb_api.xml @ 1:4a89ba6cfc63 draft

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
author jjohnson
date Tue, 25 Feb 2020 17:37:34 -0500
parents 991424605492
children 883cdf0ffae5
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0:991424605492 1:4a89ba6cfc63
1 <tool id="iedb_api" name="IEDB" version="0.1.0"> 1 <tool id="iedb_api" name="IEDB" version="2.15.0">
2 <description>MHC Binding prediction</description> 2 <description>MHC Binding prediction</description>
3 <macros>
4 <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples="">
5 <conditional name="alleles">
6 <param name="allelesrc" type="select" label="Alleles">
7 <option value="history">From history</option>
8 <option value="entry">Entered</option>
9 </param>
10 <when value="history">
11 <param name="allele_file" type="data" format="txt" label="Alleles file">
12 <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>
13 </param>
14 </when>
15 <when value="entry">
16 <param name="allele_text" type="text" size="80" label="Alleles">
17 <help>Enter alleles separated by white space: @HLA_EXAMPLES@ (The peptide lengths may follow each allele: @HLALEN_EXAMPLES@)</help>
18 <validator type="regex" message="Doesn't appear to be a valid allele">^@HLA_REGEX@(\s+@HLA_REGEX@)*$</validator>
19 </param>
20 </when>
21 </conditional>
22 </xml>
23 </macros>
3 <requirements> 24 <requirements>
25 <requirement type="package" version="3.7">python</requirement>
4 </requirements> 26 </requirements>
5 <stdio> 27 <command detect_errors="exit_code"><![CDATA[
6 <exit_code range="1:" />
7 </stdio>
8 <command interpreter="python"><![CDATA[
9 #import re 28 #import re
10 iedb_api.py --prediction=$prediction.tool --method=$prediction.method 29 python '${__tool_directory__}/iedb_api.py'
30 --prediction=$prediction.tool
31 --method=$prediction.method
32 #if $prediction.tool == 'bcell':
33 #if $prediction.window_size:
34 -w $prediction.window_size
35 #end if
36 #else
37 #if $prediction.tool == 'processing' and $prediction.proteasome:
38 --proteasome $prediction.proteasome
39 #end if
40 #if $prediction.alleles.allelesrc == 'history':
41 #for $line in open(str($prediction.alleles.allele_file)):
42 #set $fields = $line.strip().split(',')
43 #set $allele = $fields[0].strip()
44 #if len($allele) > 0:
45 #if len($fields) > 1:
46 #for $alen in $fields[1:]:
47 -a '$allele' -l $alen
48 #end for
49 #else:
50 #for $alen in str($prediction.lengths).split(','):
51 -a '$allele' -l $alen
52 #end for
53 #end if
54 #end if
55 #end for
56 #else:
57 #for $word in str($prediction.alleles.allele_text).strip().split():
58 #set $fields = $word.strip().split(',')
59 #set $allele = $fields[0].strip()
60 #if len($allele) > 0:
61 #if len($fields) > 1:
62 #for $alen in $fields[1:]:
63 -a '$allele' -l $alen
64 #end for
65 #else:
66 #for $alen in str($prediction.lengths).split(','):
67 -a '$allele' -l $alen
68 #end for
69 #end if
70 #end if
71 #end for
72 #end if
73 #end if
74
11 #if $sequence.seqsrc == 'fasta': 75 #if $sequence.seqsrc == 'fasta':
12 -i $sequence.seq_fasta 76 -i '$sequence.seq_fasta'
13 #else if $sequence.seqsrc == 'tabular': 77 #else if $sequence.seqsrc == 'tabular':
14 -i $sequence.seq_tsv 78 -i '$sequence.seq_tsv'
15 -c #echo int(str($sequence.pep_col)) - 1 79 -c #echo int(str($sequence.pep_col)) - 1
16 #if $sequence.id_col: 80 #if $sequence.id_col:
17 -C #echo int(str($sequence.id_col)) - 1 81 -C #echo int(str($sequence.id_col)) - 1
18 #end if 82 #end if
19 #else: 83 #else:
20 #for $seq in str($sequence.seq_text).strip().split(): 84 #for $seq in str($sequence.seq_text).strip().split():
21 -s $seq.strip() 85 -s $seq.strip()
22 #end for 86 #end for
23 #end if 87 #end if
24 #if $alleles.allelesrc == 'history':
25 #for $line in open(str($alleles.allele_file)):
26 #set $fields = $line.strip().split(',')
27 #set $allele = $fields[0].strip()
28 #if len($allele) > 0:
29 #if len($fields) > 1:
30 #for $alen in $fields[1:]:
31 -a $allele -l $alen
32 #end for
33 #else:
34 #for $alen in str($lengths).split(','):
35 -a $allele -l $alen
36 #end for
37 #end if
38 #end if
39 #end for
40 #else:
41 #for $word in str($alleles.allele_text).strip().split():
42 #set $fields = $word.strip().split(',')
43 #set $allele = $fields[0].strip()
44 #if len($allele) > 0:
45 #if len($fields) > 1:
46 #for $alen in $fields[1:]:
47 -a $allele -l $alen
48 #end for
49 #else:
50 #for $alen in str($lengths).split(','):
51 -a $allele -l $alen
52 #end for
53 #end if
54 #end if
55 #end for
56 #end if
57 -o $output 88 -o $output
58 ]]></command> 89 ]]></command>
59 <inputs> 90 <inputs>
91 <conditional name="prediction">
92 <param name="tool" type="select" label="Prediction">
93 <option value="mhci">MHC-I Binding</option>
94 <option value="mhcii">MHC-II Binding</option>
95 <option value="processing">MHC-I Processing</option>
96 <option value="mhcnp">MHC-NP T-Cell Epitope</option>
97 <option value="bcell">Antibody Epitope Prediction</option>
98 </param>
99 <when value="mhci">
100 <param name="method" type="select" label="prediction method">
101 <option value="recommended" selected="true">recommended</option>
102 <option value="consensus">consensus</option>
103 <option value="netmhcpan">netmhcpan</option>
104 <option value="ann">ann</option>
105 <option value="smmpmbec">smmpmbec</option>
106 <option value="smm">smm</option>
107 <option value="comblib_sidney2008">comblib_sidney2008</option>
108 <option value="netmhccons">netmhccons</option>
109 <option value="pickpocket">pickpocket</option>
110 </param>
111 <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"/>
112 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
113 <help>Used for any alleles which don't include specified lengths</help>
114 <option value="8" selected="true">8</option>
115 <option value="9">9</option>
116 <option value="10">10</option>
117 <option value="11">11</option>
118 <option value="12">12</option>
119 <option value="13">13</option>
120 <option value="14">14</option>
121 <option value="15">15</option>
122 </param>
123
124 </when>
125 <when value="mhcii">
126 <param name="method" type="select" label="prediction method">
127 <option value="recommended" selected="true">recommended</option>
128 <option value="consensus3">consensus3</option>
129 <option value="NetMHCIIpan">NetMHCIIpan</option>
130 <option value="nn_align">nn_align</option>
131 <option value="smm_align">smm_align</option>
132 <option value="comblib">comblib</option>
133 <option value="tepitope">tepitope</option>
134 </param>
135 <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]|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"/>
136 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
137 <help>Used for any alleles which don't include specified lengths</help>
138 <option value="asis">asis</option>
139 <option value="11">11</option>
140 <option value="12">12</option>
141 <option value="13">13</option>
142 <option value="14">14</option>
143 <option value="15" selected="true">15</option>
144 <option value="16">16</option>
145 <option value="17">17</option>
146 <option value="18">18</option>
147 <option value="19">19</option>
148 <option value="20">20</option>
149 <option value="21">21</option>
150 <option value="22">22</option>
151 <option value="23">23</option>
152 <option value="24">24</option>
153 <option value="25">25</option>
154 <option value="26">26</option>
155 <option value="27">27</option>
156 <option value="28">28</option>
157 <option value="29">29</option>
158 <option value="30">30</option>
159 </param>
160 </when>
161 <when value="processing">
162 <param name="method" type="select" label="prediction method">
163 <option value="recommended" selected="true">recommended</option>
164 <option value="consensus">consensus</option>
165 <option value="netmhcpan">netmhcpan</option>
166 <option value="ann">ann</option>
167 <option value="smmpmbec">smmpmbec</option>
168 <option value="smm">smm</option>
169 <option value="comblib_sidney2008">comblib_sidney2008</option>
170 </param>
171 <param name="proteasome" type="select" label="proteasome type">
172 <option value="immuno">immuno</option>
173 <option value="constitutive">constitutive</option>
174 </param>
175 <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"/>
176 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
177 <help>Used for any alleles which don't include specified lengths</help>
178 <option value="8" selected="true">8</option>
179 <option value="9">9</option>
180 <option value="10">10</option>
181 <option value="11">11</option>
182 <option value="12">12</option>
183 <option value="13">13</option>
184 <option value="14">14</option>
185 </param>
186 </when>
187 <when value="mhcnp">
188 <param name="method" type="select" label="prediction method">
189 <option value="mhcnp" selected="true">mhcnp</option>
190 <option value="netmhcpan">netmhcpan</option>
191 </param>
192 <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"/>
193 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
194 <help>Used for any alleles which don't include specified lengths</help>
195 <option value="8" selected="true">8</option>
196 <option value="9">9</option>
197 <option value="10">10</option>
198 <option value="11">11</option>
199 </param>
200 </when>
201 <when value="bcell">
202 <param name="method" type="select" label="prediction method">
203 <option value="Bepipred" selected="true">Bepipred</option>
204 <option value="Chou-Fasman">Chou-Fasman</option>
205 <option value="Emini">Emini</option>
206 <option value="Karplus-Schulz">Karplus-Schulz</option>
207 <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option>
208 <option value="Parker">Parker</option>
209 </param>
210 <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"/>
211 </when>
212 </conditional>
60 <conditional name="sequence"> 213 <conditional name="sequence">
61 <param name="seqsrc" type="select" label="Peptide sequences"> 214 <param name="seqsrc" type="select" label="Peptide sequences">
62 <option value="fasta">Fasta file</option> 215 <option value="fasta">Fasta file</option>
63 <option value="tabular">From tabular</option> 216 <option value="tabular">From tabular</option>
64 <option value="entry"></option> 217 <option value="entry"></option>
73 </when> 226 </when>
74 <when value="entry"> 227 <when value="entry">
75 <param name="seq_text" type="text" size="80" label="Peptide Sequence"/> 228 <param name="seq_text" type="text" size="80" label="Peptide Sequence"/>
76 </when> 229 </when>
77 </conditional> 230 </conditional>
78 <conditional name="alleles"> 231
79 <param name="allelesrc" type="select" label="Alleles">
80 <option value="history">From history</option>
81 <option value="entry">Entered</option>
82 </param>
83 <when value="history">
84 <param name="allele_file" type="data" format="txt" label="Alleles file">
85 <help>The dataset should have on allele per line. The allele may be followed by an optional comma-separated list of pepttide lengths, e.g.: HLA-A*02:01,8,9</help>
86 </param>
87 </when>
88 <when value="entry">
89 <param name="allele_text" type="text" size="80" label="Alleles">
90 <help>Enter alleles separated by white space: HLA-A*03:01 HLA-B*07:02 (The peptide lengths may follow each allele: HLA-A*03:01,8,9,10 HLA-B*07:02,9</help>
91 <validator type="regex" message="IDs separted by commas">^(HLA-([A-C]|D[PQR][AB]1)\*[0-9][[0-9]:[0-9][0-9](,(8|9|10|11|12|13|14|15))*)(\s+HLA-([A-C]|D[PQR][AB]1)\*[0-9][[0-9]:[0-9][0-9](,(8|9|10|11|12|13|14|15))*)*$</validator>
92 </param>
93 </when>
94 </conditional>
95 <param name="lengths" type="select" multiple="true" label="peptide lengths for prediction">
96 <help>Used for any alleles which don't include specified lengths</help>
97 <option value="8">8</option>
98 <option value="9">9</option>
99 <option value="10">10</option>
100 <option value="11">11</option>
101 <option value="12">12</option>
102 <option value="13">13</option>
103 <option value="14">14</option>
104 <option value="15">15</option>
105 </param>
106 <conditional name="prediction">
107 <param name="tool" type="select" label="Prediction">
108 <option value="mhci">MHC-I Binding</option>
109 <option value="mhcii">MHC-II Binding</option>
110 <option value="processing">MHC-I Processing</option>
111 <option value="mhcnp">MHC-NP T-Cell Epitope</option>
112 <option value="bcell">Antibody Epitope Prediction</option>
113 </param>
114 <when value="mhci">
115 <param name="method" type="select" label="prediction method">
116 <option value="recommended" selected="true">recommended</option>
117 <option value="consensus">consensus</option>
118 <option value="netmhcpan">netmhcpan</option>
119 <option value="ann">ann</option>
120 <option value="smmpmbec">smmpmbec</option>
121 <option value="smm">smm</option>
122 <option value="comblib_sidney2008">comblib_sidney2008</option>
123 <option value="netmhccons">netmhccons</option>
124 <option value="pickpocket">pickpocket</option>
125 </param>
126 </when>
127 <when value="mhcii">
128 <param name="method" type="select" label="prediction method">
129 <option value="recommended" selected="true">recommended</option>
130 <option value="consensus3">consensus3</option>
131 <option value="NetMHCIIpan">NetMHCIIpan</option>
132 <option value="nn_align">nn_align</option>
133 <option value="smm_align">smm_align</option>
134 <option value="comblib">comblib</option>
135 <option value="tepitope">tepitope</option>
136 </param>
137 </when>
138 <when value="processing">
139 <param name="method" type="select" label="prediction method">
140 <option value="recommended" selected="true">recommended</option>
141 <option value="consensus">consensus</option>
142 <option value="netmhcpan">netmhcpan</option>
143 <option value="ann">ann</option>
144 <option value="smmpmbec">smmpmbec</option>
145 <option value="smm">smm</option>
146 <option value="comblib_sidney2008">comblib_sidney2008</option>
147 </param>
148 </when>
149 <when value="mhcnp">
150 <param name="method" type="select" label="prediction method">
151 <option value="mhcnp" selected="true">mhcnp</option>
152 </param>
153 </when>
154 <when value="bcell">
155 <param name="method" type="select" label="prediction method">
156 <option value="Bepipred" selected="true">Bepipred</option>
157 <option value="Chou-Fasman">Chou-Fasman</option>
158 <option value="Emini">Emini</option>
159 <option value="Karplus-Schulz">Karplus-Schulz</option>
160 <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option>
161 <option value="Parker">Parker</option>
162 </param>
163 <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"/>
164 </when>
165 </conditional>
166 </inputs> 232 </inputs>
167 <outputs> 233 <outputs>
234 <!--
168 <data name="output" format="tabular"/> 235 <data name="output" format="tabular"/>
236 -->
237 <data name="output" format="tabular" label="IEDB ${prediction.tool} ${prediction.method}"/>
238 <data name="output2" format="tabular" label="IEDB ${prediction.tool} ${prediction.method} residue scores" from_work_dir="iedb_results2">
239 <filter>prediction['method'].startswith('Bepipred')</filter>
240 </data>
169 </outputs> 241 </outputs>
170 <tests> 242 <tests>
171 <test> 243 <!-- test1 -->
172 <param name="seqsrc" value="entry"/> 244 <test>
173 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> 245 <conditional name="prediction">
174 <param name="allelesrc" value="entry"/> 246 <param name="tool" value="mhci"/>
175 <param name="allele_text" value="HLA-A*01:01,9"/> 247 <param name="method" value="recommended"/>
176 <param name="tool" value="mhci"/> 248 <conditional name="alleles">
177 <param name="method" value="recommended"/> 249 <param name="allelesrc" value="entry"/>
250 <param name="allele_text" value="HLA-A*01:01,9"/>
251 </conditional>
252 </conditional>
253 <conditional name="sequence">
254 <param name="seqsrc" value="entry"/>
255 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
256 </conditional>
178 <output name="output"> 257 <output name="output">
179 <assert_contents> 258 <assert_contents>
180 <has_text text="LYNTVATLY" /> 259 <has_text text="LYNTVATLY" />
181 </assert_contents> 260 </assert_contents>
182 </output> 261 </output>
183 </test> 262 </test>
184 <test> 263 <!-- test2 -->
185 <param name="seqsrc" value="fasta"/> 264 <test>
186 <param name="seq_fasta" ftype="fasta" value="seqs.fa"/> 265 <conditional name="prediction">
187 <param name="allelesrc" value="history"/> 266 <param name="tool" value="mhci"/>
188 <param name="allele_file" ftype="txt" value="alleles.txt"/> 267 <param name="method" value="recommended"/>
189 <param name="tool" value="mhci"/> 268 <conditional name="alleles">
190 <param name="method" value="recommended"/> 269 <param name="allelesrc" value="history"/>
270 <param name="allele_file" ftype="tabular" value="alleles.tsv"/>
271 </conditional>
272 </conditional>
273 <conditional name="sequence">
274 <param name="seqsrc" value="fasta"/>
275 <param name="seq_fasta" ftype="fasta" value="seqs.fa"/>
276 </conditional>
191 <output name="output"> 277 <output name="output">
192 <assert_contents> 278 <assert_contents>
193 <has_text text="peptide1" /> 279 <has_text text="peptide1" />
194 <has_text text="AHKVPRRLLK" /> 280 <has_text text="HKVPRRLLK" />
195 </assert_contents> 281 </assert_contents>
196 </output> 282 </output>
197 </test> 283 </test>
198 <test> 284 <!-- test3 -->
199 <param name="seqsrc" value="tabular"/> 285 <test>
200 <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/> 286 <conditional name="prediction">
201 <param name="pep_col" value="3"/> 287 <param name="tool" value="mhci"/>
202 <param name="id_col" value="1"/> 288 <param name="method" value="recommended"/>
203 <param name="allelesrc" value="history"/> 289 <conditional name="alleles">
204 <param name="allele_file" ftype="txt" value="alleles.txt"/> 290 <param name="allelesrc" value="history"/>
205 <param name="tool" value="mhci"/> 291 <param name="allele_file" ftype="tabular" value="alleles.tsv"/>
206 <param name="method" value="recommended"/> 292 </conditional>
293 </conditional>
294 <conditional name="sequence">
295 <param name="seqsrc" value="tabular"/>
296 <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/>
297 <param name="pep_col" value="3"/>
298 <param name="id_col" value="1"/>
299 </conditional>
207 <output name="output"> 300 <output name="output">
208 <assert_contents> 301 <assert_contents>
209 <has_text text="peptide1" /> 302 <has_text text="peptide1" />
210 <has_text text="AHKVPRRLLK" /> 303 <has_text text="HKVPRRLLK" />
304 </assert_contents>
305 </output>
306 </test>
307 <!-- test4 -->
308 <test>
309 <conditional name="prediction">
310 <param name="tool" value="mhcii"/>
311 <param name="method" value="recommended"/>
312 <conditional name="alleles">
313 <param name="allelesrc" value="entry"/>
314 <param name="allele_text" value="DPA1*01/DPB1*04:01"/>
315 </conditional>
316 <param name="lengths" value="asis"/>
317 </conditional>
318 <conditional name="sequence">
319 <param name="seqsrc" value="entry"/>
320 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
321 </conditional>
322 <output name="output">
323 <assert_contents>
324 <has_text text="LYNTVATLY" />
325 </assert_contents>
326 </output>
327 </test>
328 <!-- test5 -->
329 <test>
330 <conditional name="prediction">
331 <param name="tool" value="processing"/>
332 <param name="method" value="recommended"/>
333 <conditional name="alleles">
334 <param name="allelesrc" value="entry"/>
335 <param name="allele_text" value="HLA-A*01:01,8 HLA-A*02:01,9"/>
336 </conditional>
337 <param name="proteasome" value="constitutive"/>
338 </conditional>
339 <conditional name="sequence">
340 <param name="seqsrc" value="entry"/>
341 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
342 </conditional>
343 <output name="output">
344 <assert_contents>
345 <has_text text="LYNTVATLY" />
346 </assert_contents>
347 </output>
348 </test>
349 <!-- test6 -->
350 <test>
351 <conditional name="prediction">
352 <param name="tool" value="mhcnp"/>
353 <param name="method" value="mhcnp"/>
354 <conditional name="alleles">
355 <param name="allelesrc" value="entry"/>
356 <param name="allele_text" value="HLA-A*02:01,9"/>
357 </conditional>
358 </conditional>
359 <conditional name="sequence">
360 <param name="seqsrc" value="entry"/>
361 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
362 </conditional>
363 <output name="output">
364 <assert_contents>
365 <has_text text="LYNTVATLY" />
366 </assert_contents>
367 </output>
368 </test>
369 <!-- test7 -->
370 <test>
371 <conditional name="prediction">
372 <param name="tool" value="bcell"/>
373 <param name="method" value="Emini"/>
374 </conditional>
375 <conditional name="sequence">
376 <param name="seqsrc" value="entry"/>
377 <param name="seq_text" value="VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTE"/>
378 </conditional>
379 <output name="output">
380 <assert_contents>
381 <has_text text="VLSEGE" />
211 </assert_contents> 382 </assert_contents>
212 </output> 383 </output>
213 </test> 384 </test>
214 </tests> 385 </tests>
215 <help><![CDATA[ 386 <help><![CDATA[
216 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. 387 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.
217 388
218 This tool retrieves epitope information about input peptide sequences by using the RESTful web services provided by IEDB. 389 This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB.
219 The webservices are described at: http://tools.immuneepitope.org/main/tools-api/ 390 The webservices are described at: http://tools.immuneepitope.org/main/tools-api/
391 That page also describes how to retrieve the available HLA alleles for class of epitope binding.
220 392
221 **INPUTS** 393 **INPUTS**
222 394
223 peptide sequences from a fasta file or a column in a tabular file 395 peptide sequences from a fasta file or a column in a tabular file
224 396
225 HLA alleles either entered as text or on per line in a text file 397 HLA alleles either entered as text or one per line in a text file
226 398
227 399
228 **OUTPUTS** 400 **OUTPUTS**
229 401
230 A tabular file containing the results returned from the IEDB web service 402 A tabular file containing the results returned from the IEDB web service