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1 <tool id="PaDEL789xsf1" name="PaDEL">
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2 <description>"PaDEL Descriptor Calculation Tool"</description>
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3 <command interpreter="java -jar">PaDEL-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $3d $fingerprint $retainorder -file $output1 -log >$log </command>
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4
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5 <inputs>
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6 <param format="txt" name="input" type="data" label="sdf file"/>
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7
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8 <param name="detectaromaticity" type="select" label="Detect the aroamaticity">
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9 <option value = "-detectaromaticity" selected="TRUE" >YES</option>
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10 <option value = "" >NO</option>
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11 </param>
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12
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13 <param name="removesalt" type="select" label="Remove salt">
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14 <option value = "-removesalt" selected="TRUE" >YES</option>
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15 <option value = "" >NO</option>
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16 </param>
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17
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18 <param name="standardizenitro" type="select" label="Standardize nitro groups">
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19 <option value = "-standardizenitro" selected="TRUE" >YES</option>
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20 <option value = "" >NO</option>
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21 </param>
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22
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23 <param name="convert3d" type="select" label="convert in 3D">
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24 <option value = "" selected="TRUE" >NO</option>
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25 <option value = "-convert3d" >YES</option>
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26 </param>
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27
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28 <param name="retain3d" type="select" label="Retain 3D coordinates">
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29 <option value = "" selected="TRUE" >NO</option>
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30 <option value = "-retain3d" >YES</option>
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31
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32 </param>
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33
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34 <param name="3d" type="select" label="calculate 3d descriptors">
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35 <option value = "" selected="TRUE" >NO</option>
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36 <option value = "-3d" >YES</option>
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37 </param>
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38
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39 <param name="fingerprint" type="select" label="calculate fingerprints">
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40 <option value = "" selected="TRUE" >NO</option>
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41 <option value = "-fingerprints">YES</option>
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42 </param>
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43
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44
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45 <param name="retainorder" type="select" label="Retain molecules order">
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46 <option value = "-retainorder" selected="TRUE">YES</option>
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47 <option value = "" >NO</option>
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48 </param>
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49
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50
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51
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52 <!--
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53 <param name="3d" type="checkbox" label="Include 3D descriptors" description="add 3D descriptor" value="1" default="0" />
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54 <param name="fingerprint" type="checkbox" label="Include PubChem fingerprints" description="calculate 881 fingerprints" value="1" default="0" />
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55 -->
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56 </inputs>
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57
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58 <outputs>
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59 <data format="txt" name="output1" label="Descriptors File"/>
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60 <data format="txt" name="log" label="Log File"/>
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61 </outputs>
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62
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63 <help>
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64 run command with sdf file format only and output file will be in CSV format.
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65 </help>
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66
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67 </tool>
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