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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 <requirement type="package" version="2.18">padel</requirement>
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5
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6 </requirements>
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7
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8
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9 <description>"PaDEL Descriptor Calculation Tool"</description>
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10 <command interpreter="">
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11 #if '.smi' in $input.name
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12 /bin/mkdir $input.extra_files_path;
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13 ln -s $input $input.extra_files_path/molecule.smi;
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14 /usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log > $log ;
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15 /bin/rm -rf $input.extra_files_path;
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16 #else
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17 /usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log >$log
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18 #end if
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19 </command>
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20
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21 <inputs>
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22 <param format="sdf" name="input" type="data" label="sdf/smile/mol2 file" optional= "false"/>
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23
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24 <param name="detectaromaticity" type="select" label="Detect the aroamaticity">
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25 <option value = "-detectaromaticity" selected="TRUE" >YES</option>
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26 <option value = "" >NO</option>
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27 </param>
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28
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29 <param name="removesalt" type="select" label="Remove salt">
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30 <option value = "-removesalt" selected="TRUE" >YES</option>
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31 <option value = "" >NO</option>
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32 </param>
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33
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34 <param name="standardizenitro" type="select" label="Standardize nitro groups">
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35 <option value = "-standardizenitro" selected="TRUE" >YES</option>
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36 <option value = "" >NO</option>
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37 </param>
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38
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39 <param name="convert3d" type="select" label="convert in 3D">
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40 <option value = "" selected="TRUE" >NO</option>
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41 <option value = "-convert3d" >YES</option>
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42 </param>
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43
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44 <param name="retain3d" type="select" label="Retain 3D coordinates">
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45 <option value = "" selected="TRUE" >NO</option>
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46 <option value = "-retain3d" >YES</option>
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47
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48 </param>
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49
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50 <param name="coordinate" type="select" label="calculate 3d descriptors">
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51 <option value = "" selected="TRUE" >NO</option>
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52 <option value = "-3d" >YES</option>
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53 </param>
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54
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55 <param name="fingerprint" type="select" label="calculate fingerprints">
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56 <option value = "" selected="TRUE" >NO</option>
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57 <option value = "-fingerprints">YES</option>
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58 </param>
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59
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60
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61 <param name="retainorder" type="select" label="Retain molecules order">
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62 <option value = "-retainorder" selected="TRUE">YES</option>
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63 <option value = "" >NO</option>
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64 </param>
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65
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66
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67
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68 <!--
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69 <param name="3d" type="checkbox" label="Include 3D descriptors" description="add 3D descriptor" value="1" default="0" />
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70 <param name="fingerprint" type="checkbox" label="Include PubChem fingerprints" description="calculate 881 fingerprints" value="1" default="0" />
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71 -->
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72 </inputs>
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73
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74 <outputs>
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75 <data format="csv" name="descriptor" label="Descriptors File of $input.name "/>
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76 <data format="txt" name="log" label="Log File of $input.name"/>
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77 </outputs>
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78
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79 <help>
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80 Input may be any sdf,smile or mol2 file and output file will be in CSV format.
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81 </help>
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82
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83 </tool>
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