Mercurial > repos > luis > ball
comparison galaxy_stubs/BondOrderAssigner.xml @ 2:605370bc1def draft default tip
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author | luis |
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date | Tue, 12 Jul 2016 12:33:33 -0400 |
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1 <?xml version='1.0' encoding='UTF-8'?> | |
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> | |
3 <!--Proposed Tool Section: [Preparation]--> | |
4 <tool id="BondOrderAssigner" name="BondOrderAssigner" version="1.1.0"> | |
5 <description>computes bond order assignments for a ligand </description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">BondOrderAssigner</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="stdio"/> | |
11 <expand macro="requirements"/> | |
12 <command>BondOrderAssigner | |
13 | |
14 #if $param_i: | |
15 -i $param_i | |
16 #end if | |
17 #if $param_o: | |
18 -o $param_o | |
19 #end if | |
20 #if $param_max_sol: | |
21 -max_sol $param_max_sol | |
22 #end if | |
23 #if $param_scr_pen: | |
24 -scr_pen | |
25 #if " " in str($param_scr_pen): | |
26 "$param_scr_pen" | |
27 #else | |
28 $param_scr_pen | |
29 #end if | |
30 #end if | |
31 #if $param_non_opt: | |
32 -non_opt $param_non_opt | |
33 #end if | |
34 #if $adv_opts.adv_opts_selector=='advanced': | |
35 #if $adv_opts.param_o_id: | |
36 -o_id "$adv_opts.param_o_id" | |
37 #end if | |
38 #if $adv_opts.param_o_dir: | |
39 -o_dir "$adv_opts.param_o_dir" | |
40 #end if | |
41 #end if | |
42 </command> | |
43 <inputs> | |
44 <param name="param_i" type="data" format="mol2" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input mol2-file" help="(-i) "/> | |
45 <param name="param_max_sol" type="integer" min="0" max="100" optional="True" value="25" label="maximal number of assignments solutions to compute" help="(-max_sol) "/> | |
46 <param name="param_scr_pen" type="select" optional="True" value="Antechamber" label="penalty table (Antechamber, BALL)" help="(-scr_pen) "> | |
47 <option value="Antechamber">Antechamber</option> | |
48 <option value=" BALL"> BALL</option> | |
49 </param> | |
50 <param name="param_non_opt" type="integer" min="0" max="1" optional="True" value="0" label="compute sub-optimal assignments as well" help="(-non_opt) "/> | |
51 <expand macro="advanced_options"> | |
52 <param name="param_o_id" type="text" size="30" value="$o.id" label="output id" help="(-o_id) "> | |
53 <sanitizer> | |
54 <valid initial="string.printable"> | |
55 <remove value="'"/> | |
56 <remove value="""/> | |
57 </valid> | |
58 </sanitizer> | |
59 </param> | |
60 <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last solution" help="(-o_dir) "> | |
61 <sanitizer> | |
62 <valid initial="string.printable"> | |
63 <remove value="'"/> | |
64 <remove value="""/> | |
65 </valid> | |
66 </sanitizer> | |
67 </param> | |
68 </expand> | |
69 </inputs> | |
70 <outputs> | |
71 <data name="param_o" format="mol2"/> | |
72 </outputs> | |
73 <help>This tool computes optimal and sub-optimal bond order assignments based on an atomic penalty function for a given ligand in mol2 file format. | |
74 | |
75 Optional parameters are the maximal number of solutions to be computed ('-max_sol'), the penalty table specifiying the atomic penalty rules ('-scr_pen'),and a flag indicating if sub-optimal solutions should be computed as well ('-non_opt'). | |
76 | |
77 Output of this tool is a number of mol2 files each containing one bond order assignment. | |
78 | |
79 To upload an input file please use the upload tool (Get Data -> Upload File). | |
80 | |
81 **Further information and help** can be found in our wiki https://github.com/BALL-Project/ball/wiki/BOAConstructor_Help. | |
82 | |
83 Please cite the following: Dehof, A.K., Rurainski, A., Bui, Q.B.A., Boecker, S., Lenhof, H.-P. & Hildebrandt, A. (2011). Automated Bond Order Assignment as an Optimization Problem. Bioinformatics, 2011 | |
84 | |
85 </help> | |
86 </tool> |