Mercurial > repos > luis > ball
comparison 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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1:31013b5cd066 | 2:605370bc1def |
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1 <?xml version='1.0' encoding='UTF-8'?> | |
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> | |
3 <!--Proposed Tool Section: [ForceFields]--> | |
4 <tool id="ResidueChecker" name="ResidueChecker" version="1.1.0"> | |
5 <description>check residues to debug a protein structure wrt to PDB conventions</description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">ResidueChecker</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="stdio"/> | |
11 <expand macro="requirements"/> | |
12 <command>ResidueChecker | |
13 | |
14 #if $param_pdb: | |
15 -pdb $param_pdb | |
16 #end if | |
17 #if $param_norm_names: | |
18 -norm_names $param_norm_names | |
19 #end if | |
20 #if $param_build_bonds: | |
21 -build_bonds $param_build_bonds | |
22 #end if | |
23 #if $param_frag_reconstruct: | |
24 -frag_reconstruct $param_frag_reconstruct | |
25 #end if | |
26 #if $param_extra_atoms: | |
27 -extra_atoms $param_extra_atoms | |
28 #end if | |
29 #if $param_bond_length: | |
30 -bond_length $param_bond_length | |
31 #end if | |
32 #if $param_int_net_charge: | |
33 -int_net_charge $param_int_net_charge | |
34 #end if | |
35 #if $param_large_charges: | |
36 -large_charges $param_large_charges | |
37 #end if | |
38 #if $param_large_net_charge: | |
39 -large_net_charge $param_large_net_charge | |
40 #end if | |
41 #if $param_overlapping_atoms: | |
42 -overlapping_atoms $param_overlapping_atoms | |
43 #end if | |
44 #if $param_nan_positions: | |
45 -nan_positions $param_nan_positions | |
46 #end if | |
47 #if $param_elements: | |
48 -elements $param_elements | |
49 #end if | |
50 #if $param_dublicate_atom_names: | |
51 -dublicate_atom_names $param_dublicate_atom_names | |
52 #end if | |
53 #if $param_unknown_residues: | |
54 -unknown_residues $param_unknown_residues | |
55 #end if | |
56 </command> | |
57 <inputs> | |
58 <param name="param_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-pdb) "/> | |
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"/> | |
60 <param name="param_build_bonds" type="integer" min="0" max="1" optional="True" value="0" label="add missing bonds" help="(-build_bonds) "/> | |
61 <param name="param_frag_reconstruct" type="integer" min="0" max="1" optional="True" value="0" label="reconstruct incomplete fragments" help="(-frag_reconstruct) "/> | |
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"/> | |
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) "/> | |
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) "/> | |
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) "/> | |
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) "/> | |
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) "/> | |
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) "/> | |
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) "/> | |
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) "/> | |
71 <param name="param_unknown_residues" type="integer" min="0" max="1" optional="True" value="0" label="check for unknown residues" help="(-unknown_residues) "/> | |
72 </inputs> | |
73 <expand macro="advanced_options"/> | |
74 <outputs> | |
75 <data name="param_stdout" format="text" label="Output from stdout"/> | |
76 </outputs> | |
77 <help>This tool checks the residues of a pdb file wrt. common inconsistencies such as missing atoms or suspicious distances. | |
78 | |
79 </help> | |
80 </tool> |