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1 <tool id="aaapadel001" name="PaDEL">
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2 <description>"PaDEL Descriptor Calculation Tool"</description>
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3 <command interpreter="">
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4 #if '.smi' in $input.name
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5 /bin/mkdir $input.extra_files_path;
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6 ln -s $input $input.extra_files_path/molecule.smi;
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7 /usr/bin/java -jar $__root_dir__/tools/PaDEL/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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8 /bin/rm -rf $input.extra_files_path;
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9 #else
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10 /usr/bin/java -jar $__root_dir__/tools/PaDEL/PaDEL-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log >$log
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11 #end if
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12 </command>
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13
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14 <inputs>
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15 <param format="sdf" name="input" type="data" label="sdf/smile/mol2 file" optional= "false"/>
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16
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17 <param name="detectaromaticity" type="select" label="Detect the aroamaticity">
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18 <option value = "-detectaromaticity" selected="TRUE" >YES</option>
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19 <option value = "" >NO</option>
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20 </param>
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21
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22 <param name="removesalt" type="select" label="Remove salt">
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23 <option value = "-removesalt" selected="TRUE" >YES</option>
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24 <option value = "" >NO</option>
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25 </param>
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26
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27 <param name="standardizenitro" type="select" label="Standardize nitro groups">
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28 <option value = "-standardizenitro" selected="TRUE" >YES</option>
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29 <option value = "" >NO</option>
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30 </param>
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31
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32 <param name="convert3d" type="select" label="convert in 3D">
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33 <option value = "" selected="TRUE" >NO</option>
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34 <option value = "-convert3d" >YES</option>
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35 </param>
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36
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37 <param name="retain3d" type="select" label="Retain 3D coordinates">
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38 <option value = "" selected="TRUE" >NO</option>
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39 <option value = "-retain3d" >YES</option>
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40
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41 </param>
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42
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43 <param name="coordinate" type="select" label="calculate 3d descriptors">
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44 <option value = "" selected="TRUE" >NO</option>
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45 <option value = "-3d" >YES</option>
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46 </param>
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47
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48 <param name="fingerprint" type="select" label="calculate fingerprints">
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49 <option value = "" selected="TRUE" >NO</option>
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50 <option value = "-fingerprints">YES</option>
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51 </param>
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52
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53
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54 <param name="retainorder" type="select" label="Retain molecules order">
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55 <option value = "-retainorder" selected="TRUE">YES</option>
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56 <option value = "" >NO</option>
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57 </param>
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58
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59
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60
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61 <!--
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62 <param name="3d" type="checkbox" label="Include 3D descriptors" description="add 3D descriptor" value="1" default="0" />
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63 <param name="fingerprint" type="checkbox" label="Include PubChem fingerprints" description="calculate 881 fingerprints" value="1" default="0" />
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64 -->
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65 </inputs>
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66
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67 <outputs>
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68 <data format="csv" name="descriptor" label="Descriptors File of $input.name "/>
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69 <data format="txt" name="log" label="Log File of $input.name"/>
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70 </outputs>
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71
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72 <help>
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73 Input may be any sdf,smile or mol2 file and output file will be in CSV format.
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74 </help>
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75
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76 </tool>
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