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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Preparation]-->
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4 <tool id="BondOrderAssigner" name="BondOrderAssigner" version="1.1.0">
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5 <description>computes bond order assignments for a ligand </description>
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6 <macros>
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7 <token name="@EXECUTABLE@">BondOrderAssigner</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>BondOrderAssigner
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13
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14 #if $param_i:
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15 -i $param_i
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16 #end if
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17 #if $param_o:
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18 -o $param_o
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19 #end if
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20 #if $param_max_sol:
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21 -max_sol $param_max_sol
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22 #end if
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23 #if $param_scr_pen:
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24 -scr_pen
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25 #if " " in str($param_scr_pen):
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26 "$param_scr_pen"
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27 #else
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28 $param_scr_pen
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29 #end if
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30 #end if
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31 #if $param_non_opt:
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32 -non_opt $param_non_opt
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33 #end if
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34 #if $adv_opts.adv_opts_selector=='advanced':
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35 #if $adv_opts.param_o_id:
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36 -o_id "$adv_opts.param_o_id"
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37 #end if
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38 #if $adv_opts.param_o_dir:
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39 -o_dir "$adv_opts.param_o_dir"
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40 #end if
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41 #end if
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42 </command>
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43 <inputs>
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44 <param name="param_i" type="data" format="mol2" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input mol2-file" help="(-i) "/>
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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) "/>
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46 <param name="param_scr_pen" type="select" optional="True" value="Antechamber" label="penalty table (Antechamber, BALL)" help="(-scr_pen) ">
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47 <option value="Antechamber">Antechamber</option>
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48 <option value=" BALL"> BALL</option>
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49 </param>
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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) "/>
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51 <expand macro="advanced_options">
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52 <param name="param_o_id" type="text" size="30" value="$o.id" label="output id" help="(-o_id) ">
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53 <sanitizer>
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54 <valid initial="string.printable">
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55 <remove value="'"/>
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56 <remove value="""/>
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57 </valid>
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58 </sanitizer>
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59 </param>
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60 <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last solution" help="(-o_dir) ">
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61 <sanitizer>
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62 <valid initial="string.printable">
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63 <remove value="'"/>
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64 <remove value="""/>
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65 </valid>
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66 </sanitizer>
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67 </param>
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68 </expand>
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69 </inputs>
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70 <outputs>
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71 <data name="param_o" format="mol2"/>
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72 </outputs>
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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.
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74
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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').
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76
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77 Output of this tool is a number of mol2 files each containing one bond order assignment.
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78
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79 To upload an input file please use the upload tool (Get Data -> Upload File).
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80
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81 **Further information and help** can be found in our wiki https://github.com/BALL-Project/ball/wiki/BOAConstructor_Help.
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82
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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
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84
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85 </help>
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86 </tool>
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