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annotate CADDSuite-1.5/galaxyconfigs/tools/MolPredictor.xml @ 7:bfab27640f5e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
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1
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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="molpredictor" name="MolPredictor" version="1.5">
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4 <description>predict molecule activities with QSAR model</description>
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5 <command interpreter="bash"><![CDATA[../../MolPredictor
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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( $mod ) != '' and str( $mod ) != 'None' :
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10 -mod "$mod"
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11 #end if
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12 #if str( $o ) != '' and str( $o ) != 'None' :
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13 -o "$o"
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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( $csv_cl ) != '' and str( $csv_cl ) != 'None' :
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28 -csv_cl
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29 #end if
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30 #if str( $csv_dl ) != '' and str( $csv_dl ) != 'None' :
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31 -csv_dl
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32 #end if
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33 #if str( $rm ) != '' and str( $rm ) != 'None' :
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34 -rm
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35 #end if
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36 | tail -n 5
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37 ]]></command>
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38 <inputs>
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39 <param name="i" optional="false" label="input sd-file" type="data" format="sdf"/>
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40 <param name="mod" optional="false" label="file containing QSAR model" type="data" format="mod"/>
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41 <param name="csv" optional="true" label="input csv-file w/ additional descriptors" type="data" format="csv"/>
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42 <param name="csv_nr" optional="true" label="Optional: no. of response variables in csv-file" type="text" area="true" size="1x5" value=""/>
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43 <param name="csv_sep" optional="true" label="Optional: separator symbol in csv-file" type="text" area="true" size="1x5" value=""/>
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44 <param name="sdp" optional="true" label="use sd-properties as additional descriptors" type="boolean" truevalue="true" falsevalue=""/>
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45 <param name="csv_cl" optional="true" label="csv-file has compound (row) labels" type="boolean" truevalue="true" falsevalue=""/>
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46 <param name="csv_dl" optional="true" label="csv-file has descriptor (column) labels" type="boolean" truevalue="true" falsevalue=""/>
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47 <param name="rm" optional="true" label="remove input sd-file when finished" type="boolean" truevalue="true" falsevalue=""/>
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48 </inputs>
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49 <outputs>
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50 <data name="o" format="sdf"/>
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51 </outputs>
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52 <help>This tool predictes the response values of compounds in the given molecule file using the specified QSAR model.
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53
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54 Input of this tool is a molecule file (sdf,mol2,drf) and a model-file as generated by ModelCreator or FeatureSelector.
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55 Features for all molecules in the input file are generated automatically. However, if you used an additional, externally generated feature-set to generate your QSAR model, make sure to generate features in the same manner (i.e. using the same external tool with the same settings) for the molecule file to be used here and specify the csv-file with the above options.
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56
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57 Output of this tool (as specified by '-o') is a molecule file containing the predicted values as a property tag named 'predicted_activity'.</help>
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58 </tool>