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comparison galaxy_stubs/SLICK.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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1:31013b5cd066 2:605370bc1def
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: [Scoring]-->
4 <tool id="SLICK" name="SLICK" version="1.1.0">
5 <description>scoring protein-carbohydrate interactions</description>
6 <macros>
7 <token name="@EXECUTABLE@">SLICK</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>SLICK
13
14 #if $param_rec:
15 -rec $param_rec
16 #end if
17 #if $param_lig:
18 -lig $param_lig
19 #end if
20 #if $param_cr:
21 -cr $param_cr
22 #end if
23 #if $param_pr:
24 -pr $param_pr
25 #end if
26 #if $param_lj:
27 -lj $param_lj
28 #end if
29 #if $param_op:
30 -op $param_op
31 #end if
32 #if $param_v:
33 -v $param_v
34 #end if
35 #if $param_s:
36 -s $param_s
37 #end if
38 #if $param_t:
39 -t $param_t
40 #end if
41 #if $param_E:
42 -E $param_E
43 #end if
44 #if $param_S:
45 -S $param_S
46 #end if
47 #if $param_u:
48 -u $param_u
49 #end if
50 #if $param_n:
51 -n $param_n
52 #end if
53 #if $param_N:
54 -N $param_N
55 #end if
56 #if $param_log:
57 -log $param_log
58 #end if
59 </command>
60 <inputs>
61 <param name="param_rec" type="data" format="" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input receptor file" help="(-rec) "/>
62 <param name="param_lig" type="data" format="" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input ligand file" help="(-lig) "/>
63 <param name="param_cr" type="data" format="" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="charge rules" help="(-cr) "/>
64 <param name="param_pr" type="data" format="" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="radius rules for the polar solvation" help="(-pr) "/>
65 <param name="param_lj" type="data" format="" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="use FILE for LJ parameters" help="(-lj) "/>
66 <param name="param_op" type="data" format="ini" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="read options from FILE (command line overrides!)" help="(-op) "/>
67 <param name="param_v" type="integer" value="0" label="verbosity to level" help="(-v) "/>
68 <param name="param_s" type="float" value="0.0" label="scaling factor for receptor charges" help="(-s) "/>
69 <param name="param_t" type="float" value="0.0" label="scaling factor for ligand charges" help="(-t) "/>
70 <param name="param_E" type="integer" min="0" max="1" optional="True" value="0" label="compute only SLICKEnergy" help="(-E) "/>
71 <param name="param_S" type="integer" min="0" max="1" optional="True" value="0" label="compute only SLICKScore" help="(-S) "/>
72 <param name="param_u" type="integer" min="0" max="1" optional="True" value="0" label="unite atoms" help="(-u) "/>
73 <param name="param_n" type="integer" min="0" max="1" optional="True" value="0" label="read radius rules for the nonpolar solvation from FILE" help="(-n) "/>
74 <param name="param_N" type="integer" min="0" max="1" optional="True" value="0" label="scale nonpolar radii by FACTOR" help="(-N) "/>
75 <param name="param_log" type="integer" min="0" max="1" optional="True" value="0" label="write log file" help="(-log) "/>
76 </inputs>
77 <expand macro="advanced_options"/>
78 <outputs>
79 <data name="param_stdout" format="text" label="Output from stdout"/>
80 </outputs>
81 <help>This tool calculates the SLICKEnergy / SLICK Score for protein-carbohydrate complexes.
82
83 </help>
84 </tool>