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comparison galaxy_stubs/PDBRMSDCalculator.xml @ 2:605370bc1def draft default tip

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author luis
date Tue, 12 Jul 2016 12:33:33 -0400
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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: [Docking]-->
4 <tool id="PDBRMSDCalculator" name="PDBRMSDCalculator" version="1.1.0">
5 <description>computes RMSD between protein poses </description>
6 <macros>
7 <token name="@EXECUTABLE@">PDBRMSDCalculator</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>PDBRMSDCalculator
13
14 #if $param_i_pdb:
15 -i_pdb $param_i_pdb
16 #end if
17 #if $param_i_query:
18 -i_query $param_i_query
19 #end if
20 #if $param_i_type:
21 -i_type
22 #if " " in str($param_i_type):
23 "$param_i_type"
24 #else
25 $param_i_type
26 #end if
27 #end if
28 #if $param_o:
29 -o $param_o
30 #end if
31 #if $param_scope:
32 -scope
33 #if " " in str($param_scope):
34 "$param_scope"
35 #else
36 $param_scope
37 #end if
38 #end if
39 #if $param_rmsd_type:
40 -rmsd_type
41 #if " " in str($param_rmsd_type):
42 "$param_rmsd_type"
43 #else
44 $param_rmsd_type
45 #end if
46 #end if
47 </command>
48 <inputs>
49 <param name="param_i_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb-file" help="(-i_pdb) "/>
50 <param name="param_i_query" type="data" format="dcd,txt,pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="molecule(s) to compare input file" help="(-i_query) "/>
51 <param name="param_i_type" type="select" optional="True" value="pdb" label="query type (pdb, dcd, or transformation file (rigid_transformations)" help="(-i_type) ">
52 <option value="pdb">pdb</option>
53 <option value=" dcd"> dcd</option>
54 <option value=" rigid_transformations"> rigid_transformations</option>
55 </param>
56 <param name="param_scope" type="select" optional="True" value="C_ALPHA" label="atoms to be considered for scoreing a pose (C_ALPHA, BACKBONE, ALL_ATOMS)" help="(-scope) ">
57 <option value="C_ALPHA">C_ALPHA</option>
58 <option value=" BACKBONE"> BACKBONE</option>
59 <option value=" ALL_ATOMS"> ALL_ATOMS</option>
60 </param>
61 <param name="param_rmsd_type" type="select" optional="True" value="SNAPSHOT_RMSD" label="rmsd type used for clustering (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE)" help="(-rmsd_type) ">
62 <option value="SNAPSHOT_RMSD">SNAPSHOT_RMSD</option>
63 <option value=" RIGID_RMSD"> RIGID_RMSD</option>
64 <option value=" CENTER_OF_MASS_DISTANCE"> CENTER_OF_MASS_DISTANCE</option>
65 </param>
66 </inputs>
67 <expand macro="advanced_options"/>
68 <outputs>
69 <data name="param_o" format="txt"/>
70 </outputs>
71 <help>This tool computes the RMSD between proteins.
72
73 Parameters are either a second input file (i_query) who's type has to be specified (i_type) and can be either a single pdb, a dcd or a transformation file. Optional parameters are the rmsd type (-rmsd_type), and the type of atoms used for scoring a pose (-scope).
74
75 Output of this tool is a either the rmsd (in the pdb-pdb case) or a file (-o) containing the RMSD between the first pose and all other poses.
76
77 </help>
78 </tool>