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comparison fpocket.xml @ 0:2063e965531c draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
author bgruening
date Mon, 12 Aug 2019 13:27:10 -0400
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children 909c8763f127
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-1:000000000000 0:2063e965531c
1 <tool id="fpocket" name="fpocket" version="0.1.0">
2 <description>- find potential binding sites in protein structures</description>
3 <requirements>
4 <requirement type="package" version="3.1.3">fpocket</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7
8 ln -s '$input' ./input.pdb &&
9 fpocket
10 -f ./input.pdb
11 #if $inp.pocket_type == 'channel':
12 -m 2.8 -M 5.5 -i 30
13 #elif $inp.pocket_type == 'external':
14 -m 3.5 -M 10 -i 30
15 #elif $inp.pocket_type == 'custom':
16 -m $inp.min -M $inp.max -i $inp.i -D $inp.D -C $inp.C -e $inp.e
17 #end if
18
19 ]]></command>
20 <inputs>
21 <param name="input" type="data" format="pdb" label="Input file" help="Protein structure file (PDB) to search."/>
22 <conditional name="inp">
23 <param name="pocket_type" type="select" label="Type of pocket to detect" help="Search for different kinds of pockets - or select 'custom' for more fine-grained control">
24 <option value="small_mol">Small molecule binding sites</option>
25 <option value="channel">Putative channels and small cavities</option>
26 <option value="external">Large, external pockets</option>
27 <option value="custom">Custom options (advanced)</option>
28 </param>
29 <when value="custom">
30 <param name="min" type="float" value="3" min="0" max="10" label="Minimum radius for an alpha sphere (angstroms)" help="An alpha sphere is an empty sphere in contact with 4 atoms in 3D space."/>
31 <param name="max" type="float" value="6" min="0" max="10" label="Maximum radius for an alpha sphere (angstroms)" help="An alpha sphere is an empty sphere in contact with 4 atoms in 3D space."/>
32 <param name="i" type="integer" value="35" min="20" max="50" label="Minimum number of alpha spheres a pocket must contain" help="Below this threshold pockets will not be listed in results"/>
33 <param name="D" type="float" value="2.4" min="0" max="10" label="Distance threshold for clustering algorithm (angstroms)" help="Alpha spheres may be clustered if they are separated by less than this distance"/>
34 <param name="C" type="select" value="s" label="Clustering method for grouping Voronoi vertices" help="Method for clustering alpha spheres">
35 <option value="s">Single linkage clustering</option>
36 <option value="m">Complete linkage clustering</option>
37 <option value="a">Average linkage clustering</option>
38 <option value="c">Centroid linkage clustering</option>
39 </param>
40 <param name="e" type="select" value="e" label="Distance measure for clustering">
41 <option value="e">Euclidean distance</option>
42 <option value="b">Manhattan distance</option>
43 </param>
44 </when>
45 <when value="small_mol"/>
46 <when value="channel"/>
47 <when value="external"/>
48 </conditional>
49 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files">
50 <option value="atoms" selected="true">PDB files containing the atoms in contact with each pocket</option>
51 <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option>
52 <option value="all_verts">PQR file containing all Voronoi vertices found</option>
53 <option value="info" selected="true">Log file containing pocket properties</option>
54 </param>
55 </inputs>
56
57 <outputs>
58 <collection type="list" name="atoms_output" label="Atoms in contact with each pocket">
59 <discover_datasets pattern="(?P&lt;designation&gt;^pocket\d+)_atm\.pdb$" directory="input_out/pockets" ext="pdb"/>
60 <filter>"atoms" in outputs</filter>
61 </collection>
62 <collection type="list" name="pock_verts_output" label="Voronoi vertices of each pocket">
63 <discover_datasets pattern="(?P&lt;designation&gt;^pocket\d+)_vert\.pqr$" directory="input_out/pockets" ext="pqr"/>
64 <filter>"pock_verts" in outputs</filter>
65 </collection>
66 <data format="pqr" name="all_verts_output" label="All Voronoi vertices found" from_work_dir="input_out/input_pockets.pqr">
67 <filter>"all_verts" in outputs</filter>
68 </data>
69 <data format="txt" name="info_output" label="Pocket properties" from_work_dir="input_out/input_info.txt">
70 <filter>"info" in outputs</filter>
71 </data>
72 </outputs>
73
74 <tests>
75 <!-- lines_diff needed because volume estimates are calculated via a Monte Carlo method and vary with each run -->
76 <test>
77 <param name="input" ftype="pdb" value="2brc.pdb"/>
78 <param name='pocket_type' value='custom' />
79 <param name="min" value="4.0"/>
80 <param name="max" value="7.0"/>
81 <param name="i" value="20" />
82 <param name="D" value="2.0"/>
83 <param name="C" value="c" />
84 <param name="e" value="b" />
85 <param name='outputs' value='pock_verts,all_verts' />
86 <output_collection name="pock_verts_output" type="list">
87 <element name="pocket2" ftype="pqr" file="pocket2_vert.pqr" lines_diff="2"/>
88 </output_collection>
89 <output name="all_verts_output" ftype="pqr" file='custom_pockets.pqr'/>
90 </test>
91 <test>
92 <param name="input" ftype="pdb" value="2brc.pdb"/>
93 <param name='pocket_type' value='small_mol' />
94 <output_collection name="atoms_output" type="list">
95 <element name="pocket1" ftype="pdb" file="pocket1_atm.pdb" lines_diff="2"/>
96 </output_collection>
97 <output name="info_output" ftype="txt" file='2brc_info.txt' lines_diff="20"/>
98 </test>
99 </tests>
100 <help><![CDATA[
101
102 Detect 'pockets' in a protein structure using the fpocket software. A potential use
103 of this tool is locating potential binding sites in a protein prior to performing
104 protein-ligand docking.
105
106 To use, upload a protein structure in PDB format and select the type of pocket to
107 detect. 'Custom options' can also be selected - this exposes all internal fpocket
108 parameters. Using this option requires some knowledge of the fpocket prediction
109 algorithm. Please consult the cited publications for more details.
110
111
112 -----
113
114 .. class:: infomark
115
116 **Input**
117
118 A protein structure in PDB format.
119
120 -----
121
122 .. class:: infomark
123
124 **Output**
125
126 Some or all of the following files:
127
128 - A collection of PDB files, one for each pocket, each containing the atoms bordering the pocket.
129 - A collection of PQR files, one for each pocket, each containing Voronoi vertices of the pocket.
130 - A single PQR file containing all Voronoi vertices for all pockets.
131 - A text file listing properties of all pockets detected.
132
133 ]]></help>
134 <citations>
135 <citation type="doi">10.1186/1471-2105-10-168</citation>
136 <citation type="doi">10.1093/nar/gkq383</citation>
137 </citations>
138 </tool>