Mercurial > repos > luis > ball
comparison galaxy_stubs/ExtractClustersFromWardTree.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: [Docking]--> | |
4 <tool id="ExtractClustersFromWardTree" name="ExtractClustersFromWardTree" version="1.1.0"> | |
5 <description>extracts docking clusters </description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">ExtractClustersFromWardTree</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="stdio"/> | |
11 <expand macro="requirements"/> | |
12 <command>ExtractClustersFromWardTree | |
13 | |
14 #if $param_i: | |
15 -i $param_i | |
16 #end if | |
17 #if $param_i_type: | |
18 -i_type "$param_i_type" | |
19 #end if | |
20 #if $param_o_out: | |
21 -o_out $param_o_out | |
22 #end if | |
23 #if $param_o_type: | |
24 -o_type | |
25 #if " " in str($param_o_type): | |
26 "$param_o_type" | |
27 #else | |
28 $param_o_type | |
29 #end if | |
30 #end if | |
31 #if $param_cutoff_type: | |
32 -cutoff_type | |
33 #if " " in str($param_cutoff_type): | |
34 "$param_cutoff_type" | |
35 #else | |
36 $param_cutoff_type | |
37 #end if | |
38 #end if | |
39 #if $param_cut_value: | |
40 -cut_value $param_cut_value | |
41 #end if | |
42 #if $param_min_size: | |
43 -min_size $param_min_size | |
44 #end if | |
45 </command> | |
46 <inputs> | |
47 <param name="param_i" type="data" format="dat" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input serialized cluster file" help="(-i) "/> | |
48 <param name="param_i_type" type="text" size="30" value="binary" label="input type (binary, text)" help="(-i_type) "> | |
49 <sanitizer> | |
50 <valid initial="string.printable"> | |
51 <remove value="'"/> | |
52 <remove value="""/> | |
53 </valid> | |
54 </sanitizer> | |
55 </param> | |
56 <param name="param_o_type" type="select" optional="True" value="index_list" label="output type (gv, json, index_list)" help="(-o_type) "> | |
57 <option value="gv">gv</option> | |
58 <option value=" json"> json</option> | |
59 <option value=" index_list"> index_list</option> | |
60 </param> | |
61 <param name="param_cutoff_type" type="select" optional="True" value="ward_distance" label="cutoff type (ward_distance, num_clusters)" help="(-cutoff_type) "> | |
62 <option value="ward_distance">ward_distance</option> | |
63 <option value=" num_clusters"> num_clusters</option> | |
64 </param> | |
65 <param name="param_cut_value" type="float" min="0.0" max="10000.0" optional="True" value="5.0" label="cut value for splitting the given WART tree using the cutoff-type (default 5.0)" help="(-cut_value) "/> | |
66 <param name="param_min_size" type="integer" min="1" max="10000" optional="True" value="1" label="minimal size of clusters (default 1)" help="(-min_size) "/> | |
67 </inputs> | |
68 <expand macro="advanced_options"/> | |
69 <outputs> | |
70 <data name="param_o_out" format="gv"/> | |
71 </outputs> | |
72 <help>This tool extracts clusters of docking poses given a dat file. | |
73 | |
74 Parameters are the filename (-i) of the serialized cluster tree, the output filename (-o_out), the output type (-o_type). The optional parameter -i_type allows to switch between binary (default) and text file for the cluster tree input, parameter -min_size allows to filter for cluster of a minimal size, parameter -cutoff_type defines the way to cut the cluster tree (either by ward distance or by a target number of clusters) using paramter -cut_value. | |
75 | |
76 Output of this tool is the extracted cluster tree, either as index list, as graph visualization (gv) input, or as json | |
77 | |
78 </help> | |
79 </tool> |