view galaxy_stubs/ResidueChecker.xml @ 2:605370bc1def draft default tip

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<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [ForceFields]-->
<tool id="ResidueChecker" name="ResidueChecker" version="1.1.0">
  <description>check residues to debug a protein structure wrt to PDB conventions</description>
  <macros>
    <token name="@EXECUTABLE@">ResidueChecker</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ResidueChecker

#if $param_pdb:
  -pdb $param_pdb
#end if
#if $param_norm_names:
  -norm_names $param_norm_names
#end if
#if $param_build_bonds:
  -build_bonds $param_build_bonds
#end if
#if $param_frag_reconstruct:
  -frag_reconstruct $param_frag_reconstruct
#end if
#if $param_extra_atoms:
  -extra_atoms $param_extra_atoms
#end if
#if $param_bond_length:
  -bond_length $param_bond_length
#end if
#if $param_int_net_charge:
  -int_net_charge $param_int_net_charge
#end if
#if $param_large_charges:
  -large_charges $param_large_charges
#end if
#if $param_large_net_charge:
  -large_net_charge $param_large_net_charge
#end if
#if $param_overlapping_atoms:
  -overlapping_atoms $param_overlapping_atoms
#end if
#if $param_nan_positions:
  -nan_positions $param_nan_positions
#end if
#if $param_elements:
  -elements $param_elements
#end if
#if $param_dublicate_atom_names:
  -dublicate_atom_names $param_dublicate_atom_names
#end if
#if $param_unknown_residues:
  -unknown_residues $param_unknown_residues
#end if
</command>
  <inputs>
    <param name="param_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb file" help="(-pdb) "/>
    <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"/>
    <param name="param_build_bonds" type="integer" min="0" max="1" optional="True" value="0" label="add missing bonds" help="(-build_bonds) "/>
    <param name="param_frag_reconstruct" type="integer" min="0" max="1" optional="True" value="0" label="reconstruct incomplete fragments" help="(-frag_reconstruct) "/>
    <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"/>
    <param name="param_bond_length" type="integer" min="0" max="1" optional="True" value="0" label="check for invalid bond length" help="(-bond_length) "/>
    <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) "/>
    <param name="param_large_charges" type="integer" min="0" max="1" optional="True" value="0" label="check for too large charges" help="(-large_charges) "/>
    <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) "/>
    <param name="param_overlapping_atoms" type="integer" min="0" max="1" optional="True" value="0" label="check for overlapptin atom positions" help="(-overlapping_atoms) "/>
    <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) "/>
    <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) "/>
    <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) "/>
    <param name="param_unknown_residues" type="integer" min="0" max="1" optional="True" value="0" label="check for unknown residues" help="(-unknown_residues) "/>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_stdout" format="text" label="Output from stdout"/>
  </outputs>
  <help>This tool checks the residues of a pdb file wrt. common inconsistencies such as missing atoms or suspicious distances.

</help>
</tool>