Mercurial > repos > luis > ball
comparison galaxy_stubs/ExtractProteinChains.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: [Preparation]--> | |
4 <tool id="ExtractProteinChains" name="ExtractProteinChains" version="1.1.0"> | |
5 <description>separate all chains of a pdb file into separate pdb files</description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">ExtractProteinChains</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="stdio"/> | |
11 <expand macro="requirements"/> | |
12 <command>ExtractProteinChains | |
13 | |
14 #if $param_pdb: | |
15 -pdb $param_pdb | |
16 #end if | |
17 #if $param_chain_id: | |
18 -chain_id "$param_chain_id" | |
19 #end if | |
20 #if $param_o: | |
21 -o $param_o | |
22 #end if | |
23 #if $adv_opts.adv_opts_selector=='advanced': | |
24 #if $adv_opts.param_o_id: | |
25 -o_id "$adv_opts.param_o_id" | |
26 #end if | |
27 #if $adv_opts.param_o_dir: | |
28 -o_dir "$adv_opts.param_o_dir" | |
29 #end if | |
30 #end if | |
31 </command> | |
32 <inputs> | |
33 <param name="param_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-pdb) "/> | |
34 <param name="param_chain_id" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="chain to extract" help="(-chain_id) "> | |
35 <sanitizer> | |
36 <valid initial="string.printable"> | |
37 <remove value="'"/> | |
38 <remove value="""/> | |
39 </valid> | |
40 </sanitizer> | |
41 </param> | |
42 <expand macro="advanced_options"> | |
43 <param name="param_o_id" type="text" size="30" value="$o.id" label="output id" help="(-o_id) "> | |
44 <sanitizer> | |
45 <valid initial="string.printable"> | |
46 <remove value="'"/> | |
47 <remove value="""/> | |
48 </valid> | |
49 </sanitizer> | |
50 </param> | |
51 <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last solution" help="(-o_dir) "> | |
52 <sanitizer> | |
53 <valid initial="string.printable"> | |
54 <remove value="'"/> | |
55 <remove value="""/> | |
56 </valid> | |
57 </sanitizer> | |
58 </param> | |
59 </expand> | |
60 </inputs> | |
61 <outputs> | |
62 <data name="param_o" format="pdb"/> | |
63 </outputs> | |
64 <help>This tool splits a pdb file into its chains. | |
65 | |
66 </help> | |
67 </tool> |