Mercurial > repos > jjohnson > iedb_api
comparison iedb_api.xml @ 1:4a89ba6cfc63 draft
"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 |
comparison
equal
deleted
inserted
replaced
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 |