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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: [Analysis]-->
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4 <tool id="ScoreAnalyzer" name="ScoreAnalyzer" version="1.1.0">
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5 <description>generate ROC or enrichment plots</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ScoreAnalyzer</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>ScoreAnalyzer
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13
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14 #if $param_mode:
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15 -mode
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16 #if " " in str($param_mode):
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17 "$param_mode"
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18 #else
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19 $param_mode
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20 #end if
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21 #end if
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22 #if $param_title:
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23 -title "$param_title"
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24 #end if
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25 #if $param_o:
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26 -o $param_o
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27 #end if
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28 #if $param_i:
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29 -i $param_i
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30 #end if
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31 #if $param_s:
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32 -s "$param_s"
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33 #end if
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34 #if $param_e:
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35 -e "$param_e"
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36 #end if
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37 #if $param_t:
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38 -t "$param_t"
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39 #end if
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40 #if $param_b:
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41 -b $param_b
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42 #end if
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43 </command>
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44 <inputs>
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45 <param name="param_mode" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="'roc', 'top50', 'scatter' or 'enrichment'" help="(-mode) ">
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46 <option value="roc">roc</option>
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47 <option value=" top50"> top50</option>
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48 <option value=" scatter"> scatter</option>
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49 <option value=" enrichment"> enrichment</option>
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50 </param>
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51 <param name="param_title" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="plot title" help="(-title) ">
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52 <sanitizer>
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53 <valid initial="string.printable">
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54 <remove value="'"/>
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55 <remove value="""/>
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56 </valid>
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57 </sanitizer>
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58 </param>
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59 <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/>
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60 <param name="param_s" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="score label" help="(-s) ">
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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 <param name="param_e" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="binding-free-energy/class label name" help="(-e) ">
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69 <sanitizer>
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70 <valid initial="string.printable">
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71 <remove value="'"/>
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72 <remove value="""/>
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73 </valid>
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74 </sanitizer>
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75 </param>
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76 <param name="param_t" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="only in case of non-binary act" help="(-t) data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder">
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77 <sanitizer>
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78 <valid initial="string.printable">
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79 <remove value="'"/>
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80 <remove value="""/>
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81 </valid>
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82 </sanitizer>
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83 </param>
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84 <param name="param_b" type="integer" min="0" max="1" optional="True" value="0" label="binary experimental activity data" help="(-b) "/>
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85 </inputs>
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86 <expand macro="advanced_options"/>
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87 <outputs>
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88 <data name="param_o" format="eps"/>
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89 </outputs>
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90 <help>This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring.
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91
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92 The type of plot to be generated must be chosen by either '-roc', '-top50', '-scatter' or '-enrichment'. The name of the property-tag that contains the scores to be evaluated (e.g. obtained by docking) is to be specified by '-s'; the name of the property-tag containing experimental data (e.g. binding-free-energy measurements or binder/non-binder info) by use '-e'. If the experimental reference data is not binary, then a threshold below which compound will be considered binders must be given with '-t'.
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93 The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
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94
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95 The output of this tool is a plot in form of an eps or png-file (as chosen).
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96
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97 </help>
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98 </tool>
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