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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: [Checks and evaluations]-->
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4 <tool id="LigCheck" name="LigCheck" version="1.1.0">
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5 <description>check molecules for errors</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">LigCheck</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>LigCheck
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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_o:
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18 -o $param_o
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19 #end if
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20 #if $param_ef:
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21 -ef $param_ef
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22 #end if
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23 #if $param_ri:
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24 -ri $param_ri
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25 #end if
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26 #if $param_ut:
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27 -ut $param_ut
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28 #end if
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29 #if $param_nc:
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30 -nc $param_nc
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31 #end if
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32 #if $param_rm:
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33 -rm $param_rm
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34 #end if
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35 </command>
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36 <inputs>
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37 <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file" help="(-i) "/>
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38 <param name="param_ef" type="float" value="0.5" label="error fraction; print error if fraction of invalid mols is large" help="(-ef) "/>
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39 <param name="param_ri" type="integer" min="0" max="1" optional="True" value="1" label="remove invalid molecules" help="(-ri) "/>
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40 <param name="param_ut" type="integer" min="0" max="1" optional="True" value="0" label="check for unique topologies" help="(-ut) "/>
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41 <param name="param_nc" type="integer" min="0" max="1" optional="True" value="0" label="no not check for unique conformations" help="(-nc) "/>
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42 <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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43 </inputs>
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44 <expand macro="advanced_options"/>
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45 <outputs>
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46 <data name="param_o" metadata_source="param_i" format="input"/>
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47 </outputs>
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48 <help>This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
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49
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50 The following checks are done for each molecule:
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51
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52 * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem)
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53 * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments.
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54 * each atom must have a valid assigned element
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55 * the molecule must be protonated (since this is necessary for docking/(re-)scoring).
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56 * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
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57 * partial charges may not contain completely senseless values (>5 or <-5).
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58 * each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies.
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59
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60 If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them.
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61
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62 </help>
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63 </tool>
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