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author jjohnson
date Mon, 28 Sep 2015 11:27:57 -0400
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1 <tool id="iedb_api" name="IEDB" version="0.1.0">
2 <description>MHC Binding prediction</description>
3 <requirements>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8 <command interpreter="python"><![CDATA[
9 #import re
10 iedb_api.py --prediction=$prediction.tool --method=$prediction.method
11 #if $sequence.seqsrc == 'fasta':
12 -i $sequence.seq_fasta
13 #else if $sequence.seqsrc == 'tabular':
14 -i $sequence.seq_tsv
15 -c #echo int(str($sequence.pep_col)) - 1
16 #if $sequence.id_col:
17 -C #echo int(str($sequence.id_col)) - 1
18 #end if
19 #else:
20 #for $seq in str($sequence.seq_text).strip().split():
21 -s $seq.strip()
22 #end for
23 #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 $output
58 ]]></command>
59 <inputs>
60 <conditional name="sequence">
61 <param name="seqsrc" type="select" label="Peptide sequences">
62 <option value="fasta">Fasta file</option>
63 <option value="tabular">From tabular</option>
64 <option value="entry"></option>
65 </param>
66 <when value="fasta">
67 <param name="seq_fasta" type="data" format="fasta" label="Peptide Sequence Fasta"/>
68 </when>
69 <when value="tabular">
70 <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/>
71 <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" />
72 <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/>
73 </when>
74 <when value="entry">
75 <param name="seq_text" type="text" size="80" label="Peptide Sequence"/>
76 </when>
77 </conditional>
78 <conditional name="alleles">
79 <param name="allelesrc" type="select" label="Alleles">
80 <option value="history">From history</option>
81 <option value="entry">Entered</option>
82 </param>
83 <when value="history">
84 <param name="allele_file" type="data" format="txt" label="Alleles file"/>
85 <help>The dataset should have on allele per line. The allele may be followed by an optional comma-separated list of pepttide lengths, e.g.: HLA-A*02:01,8,9</help>
86 </when>
87 <when value="entry">
88 <param name="allele_text" type="text" size="80" label="Alleles">
89 <help>Enter alleles separated by white space: HLA-A*03:01 HLA-B*07:02 (The peptide lengths may follow each allele: HLA-A*03:01,8,9,10 HLA-B*07:02,9</help>
90 <validator type="regex" message="IDs separted by commas">^(HLA-([A-C]|D[PQR][AB]1)\*[0-9][[0-9]:[0-9][0-9](,(8|9|10|11|12|13|14|15))*)(\s+HLA-([A-C]|D[PQR][AB]1)\*[0-9][[0-9]:[0-9][0-9](,(8|9|10|11|12|13|14|15))*)*$</validator>
91 </param>
92 </when>
93 </conditional>
94 <param name="lengths" type="select" multiple="true" label="peptide lengths for prediction">
95 <help>Used for any alleles which don't include specified lengths</help>
96 <option value="8">8</option>
97 <option value="9">9</option>
98 <option value="10">10</option>
99 <option value="11">11</option>
100 <option value="12">12</option>
101 <option value="13">13</option>
102 <option value="14">14</option>
103 <option value="15">15</option>
104 </param>
105 <conditional name="prediction">
106 <param name="tool" type="select" label="Prediction">
107 <option value="mhci">MHC-I Binding</option>
108 <option value="mhcii">MHC-II Binding</option>
109 <option value="processing">MHC-I Processing</option>
110 <option value="mhcnp">MHC-NP T-Cell Epitope</option>
111 <option value="bcell">Antibody Epitope Prediction</option>
112 </param>
113 <when value="mhci">
114 <param name="method" type="select" label="prediction method">
115 <option value="recommended" selected="true">recommended</option>
116 <option value="consensus">consensus</option>
117 <option value="netmhcpan">netmhcpan</option>
118 <option value="ann">ann</option>
119 <option value="smmpmbec">smmpmbec</option>
120 <option value="smm">smm</option>
121 <option value="comblib_sidney2008">comblib_sidney2008</option>
122 <option value="netmhccons">netmhccons</option>
123 <option value="pickpocket">pickpocket</option>
124 </param>
125 </when>
126 <when value="mhcii">
127 <param name="method" type="select" label="prediction method">
128 <option value="recommended" selected="true">recommended</option>
129 <option value="consensus3">consensus3</option>
130 <option value="NetMHCIIpan">NetMHCIIpan</option>
131 <option value="nn_align">nn_align</option>
132 <option value="smm_align">smm_align</option>
133 <option value="comblib">comblib</option>
134 <option value="tepitope">tepitope</option>
135 </param>
136 </when>
137 <when value="processing">
138 <param name="method" type="select" label="prediction method">
139 <option value="recommended" selected="true">recommended</option>
140 <option value="consensus">consensus</option>
141 <option value="netmhcpan">netmhcpan</option>
142 <option value="ann">ann</option>
143 <option value="smmpmbec">smmpmbec</option>
144 <option value="smm">smm</option>
145 <option value="comblib_sidney2008">comblib_sidney2008</option>
146 </param>
147 </when>
148 <when value="mhcnp">
149 <param name="method" type="select" label="prediction method">
150 <option value="mhcnp" selected="true">mhcnp</option>
151 </param>
152 </when>
153 <when value="bcell">
154 <param name="method" type="select" label="prediction method">
155 <option value="Bepipred" selected="true">Bepipred</option>
156 <option value="Chou-Fasman">Chou-Fasman</option>
157 <option value="Emini">Emini</option>
158 <option value="Karplus-Schulz">Karplus-Schulz</option>
159 <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option>
160 <option value="Parker">Parker</option>
161 </param>
162 <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"/>
163 </when>
164 </conditional>
165 </inputs>
166 <outputs>
167 <data name="output" format="tabular"/>
168 </outputs>
169 <tests>
170 <test>
171 <param name="seqsrc" value="entry"/>
172 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
173 <param name="allelesrc" value="entry"/>
174 <param name="allele_text" value="HLA-A*01:01,9"/>
175 <param name="tool" value="mhci"/>
176 <param name="method" value="recommended"/>
177 <output name="output">
178 <assert_contents>
179 <has_text text="LYNTVATLY" />
180 </assert_contents>
181 </output>
182 </test>
183 <test>
184 <param name="seqsrc" value="fasta"/>
185 <param name="seq_fasta" ftype="fasta" value="seqs.fa"/>
186 <param name="allelesrc" value="history"/>
187 <param name="allele_file" ftype="txt" value="alleles.txt"/>
188 <param name="tool" value="mhci"/>
189 <param name="method" value="recommended"/>
190 <output name="output">
191 <assert_contents>
192 <has_text text="peptide1" />
193 <has_text text="AHKVPRRLLK" />
194 </assert_contents>
195 </output>
196 </test>
197 <test>
198 <param name="seqsrc" value="tabular"/>
199 <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/>
200 <param name="pep_col" value="3"/>
201 <param name="id_col" value="1"/>
202 <param name="allelesrc" value="history"/>
203 <param name="allele_file" ftype="txt" value="alleles.txt"/>
204 <param name="tool" value="mhci"/>
205 <param name="method" value="recommended"/>
206 <output name="output">
207 <assert_contents>
208 <has_text text="peptide1" />
209 <has_text text="AHKVPRRLLK" />
210 </assert_contents>
211 </output>
212 </test>
213 </tests>
214 <help><![CDATA[
215 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.
216
217 This tool retrieves epitope information about input peptide sequences by using the RESTful web services provided by IEDB.
218 The webservices are described at: http://tools.immuneepitope.org/main/tools-api/
219
220 **INPUTS**
221
222 peptide sequences from a fasta file or a column in a tabular file
223
224 HLA alleles either entered as text or on per line in a text file
225
226
227 **OUTPUTS**
228
229 A tabular file containing the results returned from the IEDB web service
230
231 ]]></help>
232 <citations>
233 <citation type="doi">10.1093/nar/gku938</citation>
234 </citations>
235 </tool>