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comparison galaxy_stubs/SpatialConstraintDefiner.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="SpatialConstraintDefiner" name="SpatialConstraintDefiner" version="1.1.0">
5 <description>define spatial constraint</description>
6 <macros>
7 <token name="@EXECUTABLE@">SpatialConstraintDefiner</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>SpatialConstraintDefiner
13
14 #if $param_option:
15 -option $param_option
16 #end if
17 #if $param_i:
18 -i $param_i
19 #end if
20 #if $param_o:
21 -o $param_o
22 #end if
23 #if $param_type:
24 -type
25 #if " " in str($param_type):
26 "$param_type"
27 #else
28 $param_type
29 #end if
30 #end if
31 #if $param_n:
32 -n $param_n
33 #end if
34 #if $param_p:
35 -p $param_p
36 #end if
37 </command>
38 <inputs>
39 <param name="param_option" type="data" format="ini" optional="True" value="0" label="input configuration file" help="(-option) "/>
40 <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file" help="(-i) "/>
41 <param name="param_type" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="'fraction' or 'number' of compound atoms" help="(-type) ">
42 <option value="fraction">fraction</option>
43 <option value=" number"> number</option>
44 </param>
45 <param name="param_n" type="float" value="0.0" label="desired number/fraction of atoms in spatial area" help="(-n) "/>
46 <param name="param_p" type="float" value="0.0" label="penalty value" help="(-p) "/>
47 </inputs>
48 <expand macro="advanced_options"/>
49 <outputs>
50 <data name="param_o" format="ini"/>
51 </outputs>
52 <help>This tool allows to define spatial constraints for docking or scoring.
53
54 For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint.
55 Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this.
56
57 Output of this tool is a ini-file that contains the desired spatial constraint.
58
59 </help>
60 </tool>