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2 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
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3 <tool id="inputreader" name="InputReader" version="1.1">
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4 <description>generate QSAR data set</description>
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5 <command interpreter="bash"><![CDATA[../../InputReader
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6 #if str( $i ) != '' and str( $i ) != 'None' :
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7 -i "$i"
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8 #end if
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9 #if str( $o ) != '' and str( $o ) != 'None' :
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10 -o "$o"
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11 #end if
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12 #if str( $act ) != '' and str( $act ) != 'None' :
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13 -act "$act"
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14 #end if
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15 #if str( $csv ) != '' and str( $csv ) != 'None' :
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16 -csv "$csv"
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17 #end if
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18 #if str( $csv_nr ) != '' and str( $csv_nr ) != 'None' :
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19 -csv_nr "$csv_nr"
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20 #end if
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21 #if str( $csv_sep ) != '' and str( $csv_sep ) != 'None' :
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22 -csv_sep "$csv_sep"
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23 #end if
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24 #if str( $sdp ) != '' and str( $sdp ) != 'None' :
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25 -sdp
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26 #end if
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27 #if str( $no_cd ) != '' and str( $no_cd ) != 'None' :
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28 -no_cd
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29 #end if
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30 #if str( $no_cr ) != '' and str( $no_cr ) != 'None' :
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31 -no_cr
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32 #end if
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33 #if str( $csv_cl ) != '' and str( $csv_cl ) != 'None' :
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34 -csv_cl
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35 #end if
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36 #if str( $csv_dl ) != '' and str( $csv_dl ) != 'None' :
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37 -csv_dl
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38 #end if
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39 | tail -n 5
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40 ]]></command>
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41 <inputs>
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42 <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/>
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43 <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/>
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44 <param name="act" label="sd-property containing response values" optional="true" area="true" type="text" size="1x15"/>
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45 <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
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46 <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
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47 <param name="sdp" label="use sd-properties as additional descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
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48 <param name="no_cd" label="do not center descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
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49 <param name="no_cr" label="do not center response values" optional="true" type="boolean" truevalue="true" falsevalue=""/>
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50 <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
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51 <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
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52 </inputs>
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53 <outputs>
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54 <data name="o" format="dat"/>
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55 </outputs>
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56 <help>This tool reads input from sd-files and generate features for QSAR analysis.
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57 Activity data (response values) for a training set are taken from sd-properties of the input file; the name of this property can be specified by option '-act'.
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58 The following number of features will be automatically created for each molecule in your sd-file:
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59
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60 * 40 atom and bond count descriptors
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61 * 2 connectivity indices (Balaban and Zagreb index)
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62 * 4 partial charge descriptors
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63 * 14 surface descriptors
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64 * 133 topological descriptors (functional group counts)
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65
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66 If desired, you can also read additional descriptors from a csv-file; in this case you need to specify the file with the above options.
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67 Output of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator).</help>
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68 </tool> |
