comparison galaxy_stubs/PDBCutter.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: [Preparation]-->
4 <tool id="PDBCutter" name="PDBCutter" version="1.1.0">
5 <description>separate ligand and receptor </description>
6 <macros>
7 <token name="@EXECUTABLE@">PDBCutter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>PDBCutter
13
14 #if $param_i:
15 -i $param_i
16 #end if
17 #if $param_rec:
18 -rec $param_rec
19 #end if
20 #if $param_lig:
21 -lig $param_lig
22 #end if
23 #if $param_lig_chain:
24 -lig_chain "$param_lig_chain"
25 #end if
26 #if $param_lig_name:
27 -lig_name "$param_lig_name"
28 #end if
29
30 #if $rep_param_rm_ch:
31 -rm_ch
32 #for token in $rep_param_rm_ch:
33 #if " " in str(token):
34 "$token.param_rm_ch"
35 #else
36 $token.param_rm_ch
37 #end if
38 #end for
39 #end if
40
41 #if $rep_param_rm_res:
42 -rm_res
43 #for token in $rep_param_rm_res:
44 #if " " in str(token):
45 "$token.param_rm_res"
46 #else
47 $token.param_rm_res
48 #end if
49 #end for
50 #end if
51 </command>
52 <inputs>
53 <param name="param_i" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb-file" help="(-i) "/>
54 <param name="param_lig_chain" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="chain-name of ligand" help="(-lig_chain) ">
55 <sanitizer>
56 <valid initial="string.printable">
57 <remove value="'"/>
58 <remove value="&quot;"/>
59 </valid>
60 </sanitizer>
61 </param>
62 <param name="param_lig_name" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="ligand name" help="(-lig_name) ">
63 <sanitizer>
64 <valid initial="string.printable">
65 <remove value="'"/>
66 <remove value="&quot;"/>
67 </valid>
68 </sanitizer>
69 </param>
70 <repeat name="rep_param_rm_ch" min="0" max="1" title="param_rm_ch">
71 <param name="param_rm_ch" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="protein chains that are to be deleted" help="(-rm_ch) ">
72 <sanitizer>
73 <valid initial="string.printable">
74 <remove value="'"/>
75 <remove value="&quot;"/>
76 </valid>
77 </sanitizer>
78 </param>
79 </repeat>
80 <repeat name="rep_param_rm_res" min="0" max="1" title="param_rm_res">
81 <param name="param_rm_res" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="pdb-residues that are to be deleted (" help="(-rm_res) e.g. water or ions)">
82 <sanitizer>
83 <valid initial="string.printable">
84 <remove value="'"/>
85 <remove value="&quot;"/>
86 </valid>
87 </sanitizer>
88 </param>
89 </repeat>
90 </inputs>
91 <expand macro="advanced_options"/>
92 <outputs>
93 <data name="param_rec" format="pdb"/>
94 <data name="param_lig" format="pdb"/>
95 </outputs>
96 <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.
97
98 The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'.
99 Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'.
100
101 Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one pdb-file containing the reference ligand.
102
103 </help>
104 </tool>