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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="molfilter" name="MolFilter" version="0.9">
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4 <description>filter molecule files</description>
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5 <command interpreter="bash"><![CDATA[../../MolFilter
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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( $min_logP ) != '' and str( $min_logP ) != 'None' :
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10 -min_logP "$min_logP"
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11 #end if
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12 #if str( $max_logP ) != '' and str( $max_logP ) != 'None' :
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13 -max_logP "$max_logP"
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14 #end if
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15 #if str( $min_MW ) != '' and str( $min_MW ) != 'None' :
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16 -min_MW "$min_MW"
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17 #end if
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18 #if str( $max_MW ) != '' and str( $max_MW ) != 'None' :
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19 -max_MW "$max_MW"
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20 #end if
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21 #if str( $q ) != '' and str( $q ) != 'None' :
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22 -q "$q"
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23 #end if
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24 #if str( $min_sim ) != '' and str( $min_sim ) != 'None' :
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25 -min_sim "$min_sim"
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26 #end if
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27 #if str( $max_sim ) != '' and str( $max_sim ) != 'None' :
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28 -max_sim "$max_sim"
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29 #end if
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30 #if str( $smarts ) != '' and str( $smarts ) != 'None' :
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31 -smarts "$smarts"
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32 #end if
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33 #if str( $smarts_file ) != '' and str( $smarts_file ) != 'None' :
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34 -smarts_file "$smarts_file"
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35 #end if
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36 #if str( $o ) != '' and str( $o ) != 'None' :
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37 -o "$o"
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38 #end if
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39 -quiet
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40 #if str( $rm ) != '' and str( $rm ) != 'None' :
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41 -rm
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42 #end if
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43 | tail -n 5
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44 ]]></command>
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45 <inputs>
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46 <param name="i" optional="false" label="input molecule-file" type="data" format="mol2/sdf/drf"/>
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47 <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="txt"/>
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48 <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="txt"/>
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49 <param name="min_logP" optional="true" label="Optional: minimal logP value" type="text" area="true" size="1x5" value=""/>
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50 <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" area="true" size="1x5" value=""/>
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51 <param name="min_MW" optional="true" label="Optional: minimal molecular weight" type="text" area="true" size="1x5" value=""/>
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52 <param name="max_MW" optional="true" label="Optional: maximal molecular weight" type="text" area="true" size="1x5" value=""/>
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53 <param name="min_sim" optional="true" label="Optional: minimal average similarity" type="text" area="true" size="1x5" value=""/>
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54 <param name="max_sim" optional="true" label="Optional: maximal similarity" type="text" area="true" size="1x5" value=""/>
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55 <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/>
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56 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
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57 </inputs>
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58 <outputs>
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59 <data name="o" format="mol2/sdf/drf" format_source="i"/>
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60 </outputs>
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61 <help>MolFilter can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s).
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62
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63 Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria.</help>
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64 </tool> |
