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comparison galaxy_stubs/ExtractClustersFromWardTree.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: [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="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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="&quot;"/>
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>