Mercurial > repos > luis > ball
diff galaxy_stubs/ResidueChecker.xml @ 2:605370bc1def draft default tip
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author | luis |
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date | Tue, 12 Jul 2016 12:33:33 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/ResidueChecker.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,80 @@ +<?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="<class 'CTDopts.CTDopts._Null'>" 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>