Mercurial > repos > jjohnson > iedb_api
comparison iedb_api.xml @ 0:991424605492 draft
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
author | jjohnson |
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date | Mon, 17 Feb 2020 16:04:07 -0500 |
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children | 4a89ba6cfc63 |
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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 $output | |
58 ]]></command> | |
59 <inputs> | |
60 <conditional name="sequence"> | |
61 <param name="seqsrc" type="select" label="Peptide sequences"> | |
62 <option value="fasta">Fasta file</option> | |
63 <option value="tabular">From tabular</option> | |
64 <option value="entry"></option> | |
65 </param> | |
66 <when value="fasta"> | |
67 <param name="seq_fasta" type="data" format="fasta" label="Peptide Sequence Fasta"/> | |
68 </when> | |
69 <when value="tabular"> | |
70 <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/> | |
71 <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" /> | |
72 <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/> | |
73 </when> | |
74 <when value="entry"> | |
75 <param name="seq_text" type="text" size="80" label="Peptide Sequence"/> | |
76 </when> | |
77 </conditional> | |
78 <conditional name="alleles"> | |
79 <param name="allelesrc" type="select" label="Alleles"> | |
80 <option value="history">From history</option> | |
81 <option value="entry">Entered</option> | |
82 </param> | |
83 <when value="history"> | |
84 <param name="allele_file" type="data" format="txt" label="Alleles file"> | |
85 <help>The dataset should have on allele per line. The allele may be followed by an optional comma-separated list of pepttide lengths, e.g.: HLA-A*02:01,8,9</help> | |
86 </param> | |
87 </when> | |
88 <when value="entry"> | |
89 <param name="allele_text" type="text" size="80" label="Alleles"> | |
90 <help>Enter alleles separated by white space: HLA-A*03:01 HLA-B*07:02 (The peptide lengths may follow each allele: HLA-A*03:01,8,9,10 HLA-B*07:02,9</help> | |
91 <validator type="regex" message="IDs separted by commas">^(HLA-([A-C]|D[PQR][AB]1)\*[0-9][[0-9]:[0-9][0-9](,(8|9|10|11|12|13|14|15))*)(\s+HLA-([A-C]|D[PQR][AB]1)\*[0-9][[0-9]:[0-9][0-9](,(8|9|10|11|12|13|14|15))*)*$</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> | |
167 <outputs> | |
168 <data name="output" format="tabular"/> | |
169 </outputs> | |
170 <tests> | |
171 <test> | |
172 <param name="seqsrc" value="entry"/> | |
173 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> | |
174 <param name="allelesrc" value="entry"/> | |
175 <param name="allele_text" value="HLA-A*01:01,9"/> | |
176 <param name="tool" value="mhci"/> | |
177 <param name="method" value="recommended"/> | |
178 <output name="output"> | |
179 <assert_contents> | |
180 <has_text text="LYNTVATLY" /> | |
181 </assert_contents> | |
182 </output> | |
183 </test> | |
184 <test> | |
185 <param name="seqsrc" value="fasta"/> | |
186 <param name="seq_fasta" ftype="fasta" value="seqs.fa"/> | |
187 <param name="allelesrc" value="history"/> | |
188 <param name="allele_file" ftype="txt" value="alleles.txt"/> | |
189 <param name="tool" value="mhci"/> | |
190 <param name="method" value="recommended"/> | |
191 <output name="output"> | |
192 <assert_contents> | |
193 <has_text text="peptide1" /> | |
194 <has_text text="AHKVPRRLLK" /> | |
195 </assert_contents> | |
196 </output> | |
197 </test> | |
198 <test> | |
199 <param name="seqsrc" value="tabular"/> | |
200 <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/> | |
201 <param name="pep_col" value="3"/> | |
202 <param name="id_col" value="1"/> | |
203 <param name="allelesrc" value="history"/> | |
204 <param name="allele_file" ftype="txt" value="alleles.txt"/> | |
205 <param name="tool" value="mhci"/> | |
206 <param name="method" value="recommended"/> | |
207 <output name="output"> | |
208 <assert_contents> | |
209 <has_text text="peptide1" /> | |
210 <has_text text="AHKVPRRLLK" /> | |
211 </assert_contents> | |
212 </output> | |
213 </test> | |
214 </tests> | |
215 <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. | |
217 | |
218 This tool retrieves epitope 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/ | |
220 | |
221 **INPUTS** | |
222 | |
223 peptide sequences from a fasta file or a column in a tabular file | |
224 | |
225 HLA alleles either entered as text or on per line in a text file | |
226 | |
227 | |
228 **OUTPUTS** | |
229 | |
230 A tabular file containing the results returned from the IEDB web service | |
231 | |
232 ]]></help> | |
233 <citations> | |
234 <citation type="doi">10.1093/nar/gku938</citation> | |
235 </citations> | |
236 </tool> |