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comparison galaxy_stubs/PoseIndices2PDB.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: [Convert, combine and store]-->
4 <tool id="PoseIndices2PDB" name="PoseIndices2PDB" version="1.1.0">
5 <description>converts pose indices into PDB files </description>
6 <macros>
7 <token name="@EXECUTABLE@">PoseIndices2PDB</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>PoseIndices2PDB
13
14 #if $param_i_clust:
15 -i_clust $param_i_clust
16 #end if
17 #if $param_i_trans:
18 -i_trans $param_i_trans
19 #end if
20 #if $param_i_pdb:
21 -i_pdb $param_i_pdb
22 #end if
23 #if $param_o:
24 -o $param_o
25 #end if
26 #if $adv_opts.adv_opts_selector=='advanced':
27 #if $adv_opts.param_o_id:
28 -o_id "$adv_opts.param_o_id"
29 #end if
30 #if $adv_opts.param_o_dir:
31 -o_dir "$adv_opts.param_o_dir"
32 #end if
33 #end if
34 </command>
35 <inputs>
36 <param name="param_i_clust" type="data" format="txt" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input cluster index file" help="(-i_clust) "/>
37 <param name="param_i_trans" type="data" format="dcd" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input tranformation file" help="(-i_trans) "/>
38 <param name="param_i_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input reference pdb file" help="(-i_pdb) "/>
39 <expand macro="advanced_options">
40 <param name="param_o_id" type="text" size="30" value="$o.id" label="output file name prefix for 2nd to last pdb file" help="(-o_id) ">
41 <sanitizer>
42 <valid initial="string.printable">
43 <remove value="'"/>
44 <remove value="&quot;"/>
45 </valid>
46 </sanitizer>
47 </param>
48 <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last pdb file" help="(-o_dir) ">
49 <sanitizer>
50 <valid initial="string.printable">
51 <remove value="'"/>
52 <remove value="&quot;"/>
53 </valid>
54 </sanitizer>
55 </param>
56 </expand>
57 </inputs>
58 <outputs>
59 <data name="param_o" format="pdb"/>
60 </outputs>
61 <help>This tool converts all pose indices from a given transformation file and the corresponding reference PDBFile into separate PDBFiles.
62
63 Parameters are the input pose index file (-i_clust), the original transformation file (-i_trans), the corresponding reference pdb file (-i_pdb) and a naming schema for the resulting pdb files (-o).
64
65 Output of this tool is a set of PDBFiles representing the docking poses belonging to the given input cluster.
66
67 </help>
68 </tool>