Mercurial > repos > bioinformatics_lab_ufsc > test_tools

comparison predict_antibody_epitope.xml @ 4:dd573dcdbb03 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bioinformatics_lab_ufsc
date Mon, 08 Mar 2021 21:13:11 +0000
parents
children
comparison
equal deleted inserted replaced
3:43f31f6c3b59 4:dd573dcdbb03
1 <tool id="anti_ep_pred" name="IEDB BCELL Antibody Epitope Prediction" version="v3.0">
2 <description>BCELL IEDB Tool</description>
3 <requirements>
4 <requirement type="package" version="3.0">IEDB_BCELL</requirement>
5 <requirement type="package" version="1.0d">Netsurfp</requirement>
6 <requirement type="package">hh-suite</requirement>
7 <requirement type="package">MM-seqs2</requirement>
8 <requirement type="package">nunpy</requirement>
9 <requirement type="package" version="2.0.0">matplotlib</requirement>
10 <requirement type="package" version="0.18">scikit-learn</requirement>
11 <requirement type="package">scipy</requirement>
12 <requirement type="package" version=">2.7">Python</requirement>
13 </requirements>
14 <command interpreter="python">
15 #if $input_type.choice == "fchoice":
16 #if $win_size.cutoff != "def":
17 predict_antibody_epitope.py -m $method -f $input_type.file $png > prediction.txt
18 #else:
19 predict_antibody_epitope.py -m $method -f $input_type.file -w $win_size.threshold $png > prediction.txt
20 #end if
21 #else:
22 #if $win_size.cutoff != "def":
23 predict_antibody_epitope.py -m $method -s $input_type.swissid $png > prediction.txt
24 #else:
25 predict_antibody_epitope.py -m $method -s $input_type.swissid -w $win_size.threshold $png > prediction.txt
26 #end if
27 #end if
28 </command>
29 <inputs>
30 <conditional name="input_type">
31 <param name="choice" type="select" display="radio" label="File or Swissprot ID?" >
32 <option value="fchoice" selected="true">File</option>
33 <option value="schoice">Swissprot ID</option>
34 </param>
35 <when value="fchoice">
36 <param name="file" type="data" format="fasta" label="Fasta File" help="Fasta or multifasta with protein(s) sequênce(s)" />
37 </when>
38 <when value="schoice">
39 <param name="swissid" type="text" label="SwissprotID"/>
40 </when>
41 </conditional>
42 <param name="method" type="select" display="radio" label="Prediction method">
43 <option value="Chou-Fasman" selected="true">Chou-Fasman</option>
44 <option value="Emini">Emini</option>
45 <option value="Karplus-Schulz">Karplus-Schulz</option>
46 <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option>
47 <option value="Parker">Parker</option>
48 <option value="Bepipred">Bepipred</option>
49 <option value="Bepipred-2.0">Bepipred-2.0</option>
50 </param>
51 <conditional name="win_size" >
52 <param name="cutoff" type="select" display="radio" label="Window Size" >
53 <option value="" selected="true">Default, defined by method</option>
54 <option value="def">Set threshold</option>
55 </param>
56 <when value="def">
57 <param name="threshold" type="integer" value="6" label="Threshold"/>
58 </when>
59 </conditional>
60 <param name="png" type="select" display="radio" label="Plot png graph?">
61 <option value="--plot .">Yes</option>
62 <option value=" " selected="true">No</option>
63 </param>
64 </inputs>
65 <outputs>
66 <data name="pred" format="txt" from_work_dir="prediction.txt" label="Antibody Epitope prediction with $method - ${on_string}" />
67 <data name="png_out" format="png" label="${tool.name} Plot png: ${on_string}" >
68 <discover_datasets pattern="plot_" ext="png" visible="true" assign_primary_output="true" />
69 <filter>png == "--plot ."</filter>
70 </data>
71 </outputs>
72 <tests>
73 <test>
74 <!-- Testing Chou-Fasman method -->
75 <param name="method" value="Chou-Fasman" />
76 <param name="file" value="test/single_sequence.txt" />
77 <output name="pred" value="test/result_chou.txt" />
78 <output name="png_out" value="test/png_chou.png" />
79 </test>
80 <test>
81 <!-- Testing Emini method -->
82 <param name="method" value="Emini" />
83 <param name="file" value="test/single_sequence.txt" />
84 <output name="pred" value="test/result_emiini.txt" />
85 <output name="png_out" value="test/png_emini.png" />
86 </test>
87 <test>
88 <!-- Testing Karplus-Schulz method -->
89 <param name="method" value="Karplus-Schulz" />
90 <param name="file" value="test/multiple_sequence.txt" />
91 <output name="pred" value="test/result_karplus.txt" />
92 <output name="png_out" value="test/png_karplus.png" />
93 </test>
94 <test>
95 <!-- Testing Kolaskar-Tongaonkar method -->
96 <param name="method" value="Kolaskar-Tongaonkar" />
97 <param name="file" value="test/single_sequence.txt" />
98 <output name="pred" value="test/result_kolaskar.txt" />
99 <output name="png_out" value="test/png_kolaskar.png" />
100 </test>
101 <test>
102 <!-- Testing Parker method -->
103 <param name="method" value="Parker" />
104 <param name="file" value="test/single_sequence.txt" />
105 <output name="pred" value="test/result_parker.txt" />
106 <output name="png_out" value="test/png_parker.png" />
107 </test>
108 <test>
109 <!-- Testing Bepipred method -->
110 <param name="method" value="Bepipred" />
111 <param name="file" value="test/single_sequence.txt" />
112 <output name="pred" value="test/result_bepipred1.0.txt" />
113 <output name="png_out" value="test/png_bepipred1.0.png" />
114 </test>
115 <test>
116 <!-- Testing Bepipred 2.0 method -->
117 <param name="method" value="Bepipred-2.0" />
118 <param name="file" value="test/single_sequence.txt" />
119 <output name="pred" value="test/result_bepipred2.0.txt" />
120 <output name="png_out" value="test/png_bepipred2.0.png" />
121 </test>
122
123 </tests>
124
125 <help>
126 **How it works**
127
128 -----
129
130 **This is only bcell interface, need bcell installed on your Galaxy server**
131
132 -----
133
134 This package contains a collection of methods to predict linear B cell epitopes based on
135
136 sequence characteristics of the antigen using amino acid scales and HMMs. The collection
137
138 is a mixture of pythons scripts and linux environment specific binaries for Bepipred method.
139
140 -----
141
142 **WARNING: It's allowed only aminoacid sequences without (*) X and U, please remove it from your sequence before run.**
143
144
145 -----
146
147 **Outputs**
148
149 - **Antibody Epitope prediction** - Prediction with method and parameters informed;
150 - **Plot png** - Graphical representation of results;
151
152 -----
153
154 | We can go on forever with the darkness so far away
155 | Laboratory of Bioinformatics- UFSC - 2021
156 </help>
157 <citations>
158 <citation type="doi">10.1093/nar/gkx346</citation>
159 <citation type="doi">10.1110/ps.062405906</citation>
160 <citation type="doi">10.1186/1472-6807-7-64</citation>
161 <citation type="doi">10.1186/1745-7580-2-2</citation>
162 <citation type="doi">10.1021/bi00367a013</citation>
163 <citation type="doi">10.1016/0014-5793(90)80535-q</citation>
164 <citation type="doi">10.1002/9780470122921.ch2</citation>
165 <citation type="bibtex">@ARTICLE{Kim07aninterior-point,
166 author = {Emini EA, Hughes JV, Perlow DS, Boger J.},
167 title = {Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide.},
168 journal = {Journal of virology vol.},
169 year = {1985 },
170 volume = {8},
171 }</citation>
172 </citations>
173 </tool>