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comparison galaxy_stubs/DockPoseClustering.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="DockPoseClustering" name="DockPoseClustering" version="1.1.0">
5 <description>clusters docking poses </description>
6 <macros>
7 <token name="@EXECUTABLE@">DockPoseClustering</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>DockPoseClustering
13
14 #if $param_i_pdb:
15 -i_pdb $param_i_pdb
16 #end if
17 #if $param_i_dcd:
18 -i_dcd $param_i_dcd
19 #end if
20 #if $param_i_trans:
21 -i_trans $param_i_trans
22 #end if
23 #if $param_o_index_list:
24 -o_index_list $param_o_index_list
25 #end if
26 #if $param_o_score_matrix:
27 -o_score_matrix $param_o_score_matrix
28 #end if
29 #if $param_o_dcd:
30 -o_dcd $param_o_dcd
31 #end if
32 #if $param_rmsd_cutoff:
33 -rmsd_cutoff $param_rmsd_cutoff
34 #end if
35 #if $param_alg:
36 -alg
37 #if " " in str($param_alg):
38 "$param_alg"
39 #else
40 $param_alg
41 #end if
42 #end if
43 #if $param_scope:
44 -scope
45 #if " " in str($param_scope):
46 "$param_scope"
47 #else
48 $param_scope
49 #end if
50 #end if
51 #if $param_rmsd_type:
52 -rmsd_type
53 #if " " in str($param_rmsd_type):
54 "$param_rmsd_type"
55 #else
56 $param_rmsd_type
57 #end if
58 #end if
59 #if $param_o_red_dcd:
60 -o_red_dcd $param_o_red_dcd
61 #end if
62 #if $param_o_cluster_tree:
63 -o_cluster_tree $param_o_cluster_tree
64 #end if
65 #if $param_refine_alg:
66 -refine_alg
67 #if " " in str($param_refine_alg):
68 "$param_refine_alg"
69 #else
70 $param_refine_alg
71 #end if
72 #end if
73 #if $param_refine_rmsd_type:
74 -refine_rmsd_type
75 #if " " in str($param_refine_rmsd_type):
76 "$param_refine_rmsd_type"
77 #else
78 $param_refine_rmsd_type
79 #end if
80 #end if
81 #if $param_refine_rmsd_scope:
82 -refine_rmsd_scope
83 #if " " in str($param_refine_rmsd_scope):
84 "$param_refine_rmsd_scope"
85 #else
86 $param_refine_rmsd_scope
87 #end if
88 #end if
89 #if $param_use_refinement:
90 -use_refinement $param_use_refinement
91 #end if
92 #if $param_run_serial:
93 -run_serial $param_run_serial
94 #end if
95 #if $adv_opts.adv_opts_selector=='advanced':
96 #if $adv_opts.param_o_dcd_id:
97 -o_dcd_id "$adv_opts.param_o_dcd_id"
98 #end if
99 #if $adv_opts.param_o_dcd_dir:
100 -o_dcd_dir "$adv_opts.param_o_dcd_dir"
101 #end if
102 #end if
103 </command>
104 <inputs>
105 <param name="param_i_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb-file" help="(-i_pdb) "/>
106 <param name="param_i_dcd" type="data" format="dcd" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input dcd-file" help="(-i_dcd) "/>
107 <param name="param_i_trans" type="data" format="txt" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="or input transformation file for rigid rmsd clustering" help="(-i_trans) "/>
108 <param name="param_rmsd_cutoff" type="float" min="0.0" max="100.0" optional="True" value="5.0" label="minimal rmsd between the final clusters (default 5.0)" help="(-rmsd_cutoff) "/>
109 <param name="param_alg" type="select" optional="True" value="CLINK_DEFAYS" label="algorithm used for clustering (CLINK_DEFAYS, CLINK_ALTHAUS, NEAREST_NEIGHBOR_CHAIN_WARD, SLINK_SIBSON, TRIVIAL_COMPLETE_LINKAGE)" help="(-alg) ">
110 <option value="CLINK_DEFAYS">CLINK_DEFAYS</option>
111 <option value=" CLINK_ALTHAUS"> CLINK_ALTHAUS</option>
112 <option value=" TRIVIAL_COMPLETE_LINKAGE"> TRIVIAL_COMPLETE_LINKAGE</option>
113 <option value=" NEAREST_NEIGHBOR_CHAIN_WARD"> NEAREST_NEIGHBOR_CHAIN_WARD</option>
114 <option value=" SLINK_SIBSON"> SLINK_SIBSON</option>
115 </param>
116 <param name="param_scope" type="select" optional="True" value="C_ALPHA" label="atoms to be considered for scoreing a pose (C_ALPHA, BACKBONE, ALL_ATOMS)" help="(-scope) ">
117 <option value="C_ALPHA">C_ALPHA</option>
118 <option value=" BACKBONE"> BACKBONE</option>
119 <option value=" ALL_ATOMS"> ALL_ATOMS</option>
120 </param>
121 <param name="param_rmsd_type" type="select" optional="True" value="SNAPSHOT_RMSD" label="rmsd type used for clustering (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE)" help="(-rmsd_type) ">
122 <option value="SNAPSHOT_RMSD">SNAPSHOT_RMSD</option>
123 <option value=" RIGID_RMSD"> RIGID_RMSD</option>
124 <option value=" CENTER_OF_MASS_DISTANCE"> CENTER_OF_MASS_DISTANCE</option>
125 </param>
126 <param name="param_refine_alg" type="select" optional="True" value="CLINK_DEFAYS" label="algorithm used for second clustering run (CLINK_DEFAYS, NEAREST_NEIGHBOR_CHAIN_WARD, SLINK_SIBSON, TRIVIAL_COMPLETE_LINKAGE)" help="(-refine_alg) ">
127 <option value="CLINK_DEFAYS">CLINK_DEFAYS</option>
128 <option value=" CLINK_ALTHAUS"> CLINK_ALTHAUS</option>
129 <option value=" TRIVIAL_COMPLETE_LINKAGE"> TRIVIAL_COMPLETE_LINKAGE</option>
130 <option value=" NEAREST_NEIGHBOR_CHAIN_WARD"> NEAREST_NEIGHBOR_CHAIN_WARD</option>
131 <option value=" SLINK_SIBSON"> SLINK_SIBSON</option>
132 </param>
133 <param name="param_refine_rmsd_type" type="select" optional="True" value="SNAPSHOT_RMSD" label="rmsd type used for second clustering run (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE)" help="(-refine_rmsd_type) ">
134 <option value="SNAPSHOT_RMSD">SNAPSHOT_RMSD</option>
135 <option value=" RIGID_RMSD"> RIGID_RMSD</option>
136 <option value=" CENTER_OF_MASS_DISTANCE"> CENTER_OF_MASS_DISTANCE</option>
137 </param>
138 <param name="param_refine_rmsd_scope" type="select" optional="True" value="C_ALPHA" label="atoms to be considered for rmsd score in second clustering run (C_ALPHA, BACKBONE, ALL_ATOMS)" help="(-refine_rmsd_scope) ">
139 <option value="C_ALPHA">C_ALPHA</option>
140 <option value=" BACKBONE"> BACKBONE</option>
141 <option value=" ALL_ATOMS"> ALL_ATOMS</option>
142 </param>
143 <param name="param_use_refinement" type="integer" min="0" max="1" optional="True" value="0" label="Apply a second clustering run with different options (-refine_alg &lt;string&gt;, -refine_rmsd_type &lt;string&gt;, and -refine_rmsd_scope &lt;string&gt;)" help="(-use_refinement) "/>
144 <param name="param_run_serial" type="integer" min="0" max="1" optional="True" value="0" label="force serial excecution, even if parallel execution would be supported by the algorithm" help="(-run_serial) "/>
145 <expand macro="advanced_options">
146 <param name="param_o_dcd_id" type="text" size="30" value="$o_dcd.id" label="output id" help="(-o_dcd_id) ">
147 <sanitizer>
148 <valid initial="string.printable">
149 <remove value="'"/>
150 <remove value="&quot;"/>
151 </valid>
152 </sanitizer>
153 </param>
154 <param name="param_o_dcd_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last cluster dcd file (if needed)" help="(-o_dcd_dir) ">
155 <sanitizer>
156 <valid initial="string.printable">
157 <remove value="'"/>
158 <remove value="&quot;"/>
159 </valid>
160 </sanitizer>
161 </param>
162 </expand>
163 </inputs>
164 <outputs>
165 <data name="param_o_index_list" format="txt"/>
166 <data name="param_o_score_matrix" format="txt"/>
167 <data name="param_o_dcd" format="dcd"/>
168 <data name="param_o_red_dcd" format="dcd"/>
169 <data name="param_o_cluster_tree" format="dat"/>
170 </outputs>
171 <help>This tool computes clusters of docking poses given as conformation set or a list of rigid transformations.
172
173 Parameters are either the input ConformationSet (-i_dcd) and one corresponding pdb file (-i_pdb), or a transformation file (-i_trans). Output can be a cluster index list (-o_index_list), a cluster scoring matrix (-o_score_matrix), or dcd files per cluster (-o_dcd). Optional parameters are the algorithm (-alg), the minimal rmsd between the final clusters (-rmsd_cutoff), the rmsd type (-rmsd_type), and the type of atoms used for scoring a pose (-scope). The optional parameter -o_red_dcd sets the output file for the reduced cluster set (one representative per cluster). The optional parameter -o_cluster_tree specifies the output file for storing the cluster tree.
174
175 Output of this tool depends in the choice of the output parameters.
176
177 </help>
178 </tool>