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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: [ForceFields]-->
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4 <tool id="ResidueChecker" name="ResidueChecker" version="1.1.0">
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5 <description>check residues to debug a protein structure wrt to PDB conventions</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ResidueChecker</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>ResidueChecker
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13
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14 #if $param_pdb:
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15 -pdb $param_pdb
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16 #end if
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17 #if $param_norm_names:
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18 -norm_names $param_norm_names
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19 #end if
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20 #if $param_build_bonds:
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21 -build_bonds $param_build_bonds
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22 #end if
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23 #if $param_frag_reconstruct:
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24 -frag_reconstruct $param_frag_reconstruct
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25 #end if
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26 #if $param_extra_atoms:
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27 -extra_atoms $param_extra_atoms
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28 #end if
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29 #if $param_bond_length:
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30 -bond_length $param_bond_length
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31 #end if
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32 #if $param_int_net_charge:
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33 -int_net_charge $param_int_net_charge
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34 #end if
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35 #if $param_large_charges:
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36 -large_charges $param_large_charges
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37 #end if
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38 #if $param_large_net_charge:
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39 -large_net_charge $param_large_net_charge
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40 #end if
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41 #if $param_overlapping_atoms:
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42 -overlapping_atoms $param_overlapping_atoms
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43 #end if
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44 #if $param_nan_positions:
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45 -nan_positions $param_nan_positions
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46 #end if
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47 #if $param_elements:
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48 -elements $param_elements
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49 #end if
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50 #if $param_dublicate_atom_names:
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51 -dublicate_atom_names $param_dublicate_atom_names
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52 #end if
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53 #if $param_unknown_residues:
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54 -unknown_residues $param_unknown_residues
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55 #end if
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56 </command>
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57 <inputs>
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58 <param name="param_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-pdb) "/>
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59 <param name="param_norm_names" type="integer" min="0" max="1" optional="True" value="0" label="ensures a consistent naming scheme for all atoms," help="(-norm_names) e.g. PDB conventions"/>
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60 <param name="param_build_bonds" type="integer" min="0" max="1" optional="True" value="0" label="add missing bonds" help="(-build_bonds) "/>
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61 <param name="param_frag_reconstruct" type="integer" min="0" max="1" optional="True" value="0" label="reconstruct incomplete fragments" help="(-frag_reconstruct) "/>
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62 <param name="param_extra_atoms" type="integer" min="0" max="1" optional="True" value="0" label="check for extra atoms, i.e" help="(-extra_atoms) unknown in the reference fragment"/>
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63 <param name="param_bond_length" type="integer" min="0" max="1" optional="True" value="0" label="check for invalid bond length" help="(-bond_length) "/>
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64 <param name="param_int_net_charge" type="integer" min="0" max="1" optional="True" value="0" label="check if integer charges" help="(-int_net_charge) "/>
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65 <param name="param_large_charges" type="integer" min="0" max="1" optional="True" value="0" label="check for too large charges" help="(-large_charges) "/>
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66 <param name="param_large_net_charge" type="integer" min="0" max="1" optional="True" value="0" label="check for too large net charge" help="(-large_net_charge) "/>
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67 <param name="param_overlapping_atoms" type="integer" min="0" max="1" optional="True" value="0" label="check for overlapptin atom positions" help="(-overlapping_atoms) "/>
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68 <param name="param_nan_positions" type="integer" min="0" max="1" optional="True" value="0" label="check for ill-valued atomic positions" help="(-nan_positions) "/>
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69 <param name="param_elements" type="integer" min="0" max="1" optional="True" value="0" label="check if atom names reflect the atomic element" help="(-elements) "/>
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70 <param name="param_dublicate_atom_names" type="integer" min="0" max="1" optional="True" value="0" label="check for dublicated atom names" help="(-dublicate_atom_names) "/>
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71 <param name="param_unknown_residues" type="integer" min="0" max="1" optional="True" value="0" label="check for unknown residues" help="(-unknown_residues) "/>
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72 </inputs>
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73 <expand macro="advanced_options"/>
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74 <outputs>
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75 <data name="param_stdout" format="text" label="Output from stdout"/>
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76 </outputs>
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77 <help>This tool checks the residues of a pdb file wrt. common inconsistencies such as missing atoms or suspicious distances.
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78
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79 </help>
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80 </tool>
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