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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Preparation]-->
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4 <tool id="MolFilter" name="MolFilter" version="0.9">
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5 <description>filter molecule files </description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MolFilter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>MolFilter
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13
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14 #if $param_i:
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15 -i $param_i
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16 #end if
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17 #if $param_min_logP:
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18 -min_logP $param_min_logP
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19 #end if
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20 #if $param_max_logP:
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21 -max_logP $param_max_logP
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22 #end if
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23 #if $param_min_MW:
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24 -min_MW $param_min_MW
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25 #end if
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26 #if $param_max_MW:
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27 -max_MW $param_max_MW
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28 #end if
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29 #if $param_q:
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30 -q $param_q
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31 #end if
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32 #if $param_min_sim:
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33 -min_sim $param_min_sim
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34 #end if
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35 #if $param_max_sim:
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36 -max_sim $param_max_sim
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37 #end if
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38 #if $param_smarts:
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39 -smarts "$param_smarts"
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40 #end if
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41 #if $param_smarts_file:
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42 -smarts_file $param_smarts_file
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43 #end if
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44 #if $param_o:
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45 -o $param_o
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46 #end if
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47 #if $param_quiet:
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48 -quiet $param_quiet
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49 #end if
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50 #if $param_rm:
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51 -rm $param_rm
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52 #end if
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53 </command>
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54 <inputs>
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55 <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule-file" help="(-i) "/>
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56 <param name="param_min_logP" type="float" value="0.0" label="minimal logP value" help="(-min_logP) "/>
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57 <param name="param_max_logP" type="float" value="20.0" label="maximal logP value" help="(-max_logP) "/>
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58 <param name="param_min_MW" type="float" value="0.0" label="minimal molecular weight" help="(-min_MW) "/>
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59 <param name="param_max_MW" type="float" value="10000000000.0" label="maximal molecular weight" help="(-max_MW) "/>
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60 <param name="param_q" type="data" format="txt" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="query molecules for similarity searching" help="(-q) "/>
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61 <param name="param_min_sim" type="float" value="0.0" label="minimal average similarity" help="(-min_sim) "/>
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62 <param name="param_max_sim" type="float" value="1.0" label="maximal similarity" help="(-max_sim) "/>
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63 <param name="param_smarts" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="SMARTS pattern" help="(-smarts) ">
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64 <sanitizer>
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65 <valid initial="string.printable">
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66 <remove value="'"/>
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67 <remove value="""/>
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68 </valid>
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69 </sanitizer>
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70 </param>
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71 <param name="param_smarts_file" type="data" format="txt" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="SMARTS pattern" help="(-smarts_file) "/>
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72 <param name="param_quiet" type="integer" min="0" max="1" optional="True" value="0" label="by quiet, i.e. do not show progress information" help="(-quiet) "/>
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73 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
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74 </inputs>
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75 <expand macro="advanced_options"/>
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76 <outputs>
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77 <data name="param_o" metadata_source="param_i" format="input"/>
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78 </outputs>
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79 <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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80
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81 Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria.
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82
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83 </help>
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84 </tool>
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