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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: [Scoring]-->
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4 <tool id="SLICK" name="SLICK" version="1.1.0">
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5 <description>scoring protein-carbohydrate interactions</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SLICK</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>SLICK
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13
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14 #if $param_rec:
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15 -rec $param_rec
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16 #end if
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17 #if $param_lig:
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18 -lig $param_lig
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19 #end if
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20 #if $param_cr:
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21 -cr $param_cr
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22 #end if
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23 #if $param_pr:
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24 -pr $param_pr
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25 #end if
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26 #if $param_lj:
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27 -lj $param_lj
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28 #end if
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29 #if $param_op:
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30 -op $param_op
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31 #end if
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32 #if $param_v:
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33 -v $param_v
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34 #end if
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35 #if $param_s:
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36 -s $param_s
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37 #end if
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38 #if $param_t:
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39 -t $param_t
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40 #end if
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41 #if $param_E:
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42 -E $param_E
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43 #end if
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44 #if $param_S:
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45 -S $param_S
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46 #end if
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47 #if $param_u:
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48 -u $param_u
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49 #end if
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50 #if $param_n:
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51 -n $param_n
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52 #end if
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53 #if $param_N:
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54 -N $param_N
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55 #end if
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56 #if $param_log:
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57 -log $param_log
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58 #end if
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59 </command>
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60 <inputs>
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61 <param name="param_rec" type="data" format="" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input receptor file" help="(-rec) "/>
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62 <param name="param_lig" type="data" format="" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input ligand file" help="(-lig) "/>
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63 <param name="param_cr" type="data" format="" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="charge rules" help="(-cr) "/>
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64 <param name="param_pr" type="data" format="" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="radius rules for the polar solvation" help="(-pr) "/>
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65 <param name="param_lj" type="data" format="" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="use FILE for LJ parameters" help="(-lj) "/>
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66 <param name="param_op" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="read options from FILE (command line overrides!)" help="(-op) "/>
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67 <param name="param_v" type="integer" value="0" label="verbosity to level" help="(-v) "/>
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68 <param name="param_s" type="float" value="0.0" label="scaling factor for receptor charges" help="(-s) "/>
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69 <param name="param_t" type="float" value="0.0" label="scaling factor for ligand charges" help="(-t) "/>
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70 <param name="param_E" type="integer" min="0" max="1" optional="True" value="0" label="compute only SLICKEnergy" help="(-E) "/>
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71 <param name="param_S" type="integer" min="0" max="1" optional="True" value="0" label="compute only SLICKScore" help="(-S) "/>
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72 <param name="param_u" type="integer" min="0" max="1" optional="True" value="0" label="unite atoms" help="(-u) "/>
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73 <param name="param_n" type="integer" min="0" max="1" optional="True" value="0" label="read radius rules for the nonpolar solvation from FILE" help="(-n) "/>
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74 <param name="param_N" type="integer" min="0" max="1" optional="True" value="0" label="scale nonpolar radii by FACTOR" help="(-N) "/>
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75 <param name="param_log" type="integer" min="0" max="1" optional="True" value="0" label="write log file" help="(-log) "/>
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76 </inputs>
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77 <expand macro="advanced_options"/>
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78 <outputs>
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79 <data name="param_stdout" format="text" label="Output from stdout"/>
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80 </outputs>
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81 <help>This tool calculates the SLICKEnergy / SLICK Score for protein-carbohydrate complexes.
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82
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83 </help>
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84 </tool>
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