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1 <tool id="PaDEL789xsf1" name="PaDEL">
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2 <requirements>
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3 <requirement type="set_environment">PADEL_PATH</requirement>
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4
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5 </requirements>
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6
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7
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8 <description>"PaDEL Descriptor Calculation Tool"</description>
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9 <command interpreter="">
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10 #if '.smi' in $input.name
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11 /bin/mkdir $input.extra_files_path;
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12 ln -s $input $input.extra_files_path/molecule.smi;
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13 /usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi $coordinate2d -maxruntime $maxruntime -waitingjobs $maxjob -threads $thread-$detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d $fingerprint $retainorder -file $descriptor -log > $log ;
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14 /bin/rm -rf $input.extra_files_path;
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15 #else
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16 /usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input $coordinate2d -maxruntime $maxruntime -waitingjobs $maxjob -threads $thread $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d $fingerprint $retainorder -file $descriptor -log >$log
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17 #end if
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18 </command>
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19
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20 <inputs>
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21 <param format="sdf" name="input" type="data" label="sdf/smile/mol2 file" optional= "false"/>
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22
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23 <param name="detectaromaticity" type="select" label="Detect the aroamaticity">
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24 <option value = "-detectaromaticity" selected="TRUE" >YES</option>
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25 <option value = "" >NO</option>
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26 </param>
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27
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28 <param name="removesalt" type="select" label="Remove salt">
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29 <option value = "-removesalt" selected="TRUE" >YES</option>
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30 <option value = "" >NO</option>
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31 </param>
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32
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33 <param name="standardizenitro" type="select" label="Standardize nitro groups">
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34 <option value = "-standardizenitro" selected="TRUE" >YES</option>
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35 <option value = "" >NO</option>
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36 </param>
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37
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38 <param name="maxruntime" type="integer" value="300000" label="Set run time for individual molecule" help="in miliseconds" >
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39 <validator type="empty_field" message="This field can't be left blank"/>
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40 </param>
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41
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42 <param name="thread" type="integer" value="8" label="Workers for the job" help="set number of threads -1 for maximun " >
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43 <validator type="empty_field" message="This field can't be left blank"/>
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44 </param>
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45
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46
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47 <param name="maxjob" type="integer" value="-1" label="Maximum waiting job per thread. " help="put -1 for maximum uitility or put positive inetger values upto 50" >
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48 <validator type="empty_field" message="This field can't be left blank"/>
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49 </param>
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50
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51
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52 <param name="convert3d" type="select" label="convert in 3D">
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53 <option value = "" selected="TRUE" >NO</option>
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54 <option value = "-convert3d" >YES</option>
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55 </param>
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56
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2
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57
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58
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59 <param name="retain3d" type="select" label="Retain 3D coordinates">
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60 <option value = "" selected="TRUE" >NO</option>
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61 <option value = "-retain3d" >YES</option>
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2
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62
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63
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64 </param>
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65
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66 <param name="coordinate3d" type="select" label="calculate 3d descriptors">
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67 <option value = "" selected="TRUE" >NO</option>
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68 <option value = "-3d" >YES</option>
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69 </param>
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1
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70
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71 <param name="coordinate2d" type="select" label="calculate 2d descriptors">
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72 <option value = "" >NO</option>
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73 <option value = "-2d" selected="TRUE" >YES</option>
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74 </param>
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75
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76
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77 <param name="fingerprint" type="select" label="calculate fingerprints">
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78 <option value = "" selected="TRUE" >NO</option>
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79 <option value = "-fingerprints">YES</option>
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80 </param>
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81
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82
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83 <param name="retainorder" type="select" label="Retain molecules order">
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84 <option value = "-retainorder" selected="TRUE">YES</option>
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85 <option value = "" >NO</option>
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86 </param>
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87
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88
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89
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90 <!--
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91 <param name="3d" type="checkbox" label="Include 3D descriptors" description="add 3D descriptor" value="1" default="0" />
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92 <param name="fingerprint" type="checkbox" label="Include PubChem fingerprints" description="calculate 881 fingerprints" value="1" default="0" />
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93 -->
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94 </inputs>
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95
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96 <outputs>
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97 <data format="csv" name="descriptor" label="Descriptors File of $input.name "/>
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98 <data format="txt" name="log" label="Log File of $input.name"/>
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99 </outputs>
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100
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101 <help>
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102 Input may be any sdf,smile or mol2 file and output file will be in CSV format.
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103 </help>
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104
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105 </tool>
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