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comparison fpocket.xml @ 3:4cc9d85c3bae draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
author bgruening
date Fri, 10 Sep 2021 08:20:08 +0000
parents 4fb73be7f4cb
children
comparison
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2:4fb73be7f4cb 3:4cc9d85c3bae
1 <tool id="fpocket" name="fpocket" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="fpocket" name="fpocket" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>- find potential binding sites in protein structures</description>
2 <macros> 3 <macros>
3 <token name="@TOOL_VERSION@">3.1.4.2</token> 4 <import>macros.xml</import>
4 <token name="@GALAXY_VERSION@">0</token> 5 <token name="@GALAXY_VERSION@">0</token>
5 </macros> 6 </macros>
6 <description>- find potential binding sites in protein structures</description> 7 <expand macro="requirements" />
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">fpocket</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
11 9
12 ln -s '$input' ./input.pdb && 10 ln -s '$input' ./input.pdb &&
13 fpocket 11 fpocket
14 -f ./input.pdb 12 -f ./input.pdb
15 #if $inp.pocket_type == 'channel': 13 #if $inp.pocket_type == 'channel':
16 -m 2.8 -M 5.5 -i 30 14 --min_alpha_size 2.8 --max_alpha_size 5.5 --min_spheres_per_pocket 30
17 #elif $inp.pocket_type == 'external': 15 #elif $inp.pocket_type == 'external':
18 -m 3.5 -M 10 -i 30 16 --min_alpha_size 3.5 --max_alpha_size 10 --min_spheres_per_pocket 30
19 #elif $inp.pocket_type == 'custom': 17 #elif $inp.pocket_type == 'custom':
20 -m $inp.min -M $inp.max -i $inp.i -D $inp.D -C $inp.C -e $inp.e 18 --min_alpha_size $inp.min
19 --max_alpha_size $inp.max
20 --min_spheres_per_pocket $inp.i
21 --clustering_distance $inp.D
22 --clustering_method $inp.C
23 --clustering_measure $inp.e
21 #end if 24 #end if
22 25
23 ]]></command> 26 ]]></command>
24 <inputs> 27 <inputs>
25 <param name="input" type="data" format="pdb" label="Input file" help="Protein structure file (PDB) to search."/> 28 <param name="input" type="data" format="pdb" label="Input file" help="Protein structure file (PDB) to search."/>
26 <conditional name="inp"> 29 <expand macro="inputs" />
27 <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">
28 <option value="small_mol">Small molecule binding sites</option>
29 <option value="channel">Putative channels and small cavities</option>
30 <option value="external">Large, external pockets</option>
31 <option value="custom">Custom options (advanced)</option>
32 </param>
33 <when value="custom">
34 <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."/>
35 <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."/>
36 <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"/>
37 <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"/>
38 <param name="C" type="select" value="s" label="Clustering method for grouping Voronoi vertices" help="Method for clustering alpha spheres">
39 <option value="s">Single linkage clustering</option>
40 <option value="m">Complete linkage clustering</option>
41 <option value="a">Average linkage clustering</option>
42 <option value="c">Centroid linkage clustering</option>
43 </param>
44 <param name="e" type="select" value="e" label="Distance measure for clustering">
45 <option value="e">Euclidean distance</option>
46 <option value="b">Manhattan distance</option>
47 </param>
48 </when>
49 <when value="small_mol"/>
50 <when value="channel"/>
51 <when value="external"/>
52 </conditional>
53 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files"> 30 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files">
54 <option value="atoms" selected="true">PDB files containing the atoms in contact with each pocket</option> 31 <option value="atoms" selected="true">PDB files containing the atoms in contact with each pocket</option>
55 <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option> 32 <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option>
56 <option value="alpha_pdb" selected="true">PDB file containing alpha spheres found</option> 33 <option value="alpha_pdb" selected="true">PDB file containing alpha spheres found</option>
57 <option value="all_verts" selected="true">PQR file containing all Voronoi vertices found</option> 34 <option value="all_verts" selected="true">PQR file containing all Voronoi vertices found</option>
82 <tests> 59 <tests>
83 <!-- lines_diff needed because volume estimates are calculated via a Monte Carlo method and vary with each run --> 60 <!-- lines_diff needed because volume estimates are calculated via a Monte Carlo method and vary with each run -->
84 <test> 61 <test>
85 <param name="input" ftype="pdb" value="2brc.pdb"/> 62 <param name="input" ftype="pdb" value="2brc.pdb"/>
86 <param name='pocket_type' value='custom' /> 63 <param name='pocket_type' value='custom' />
87 <param name="min" value="4.0"/> 64 <param name="min" value="1.0"/>
88 <param name="max" value="7.0"/> 65 <param name="max" value="3.0"/>
89 <param name="i" value="20" /> 66 <param name="i" value="20" />
90 <param name="D" value="2.0"/> 67 <param name="D" value="2.0"/>
91 <param name="C" value="c" /> 68 <param name="C" value="c" />
92 <param name="e" value="b" /> 69 <param name="e" value="b" />
93 <param name='outputs' value='pock_verts,all_verts' /> 70 <param name='outputs' value='pock_verts,all_verts' />
143 - A collection of PQR files, one for each pocket, each containing Voronoi vertices of the pocket. 120 - A collection of PQR files, one for each pocket, each containing Voronoi vertices of the pocket.
144 - A single PQR file containing all Voronoi vertices for all pockets. 121 - A single PQR file containing all Voronoi vertices for all pockets.
145 - A text file listing properties of all pockets detected. 122 - A text file listing properties of all pockets detected.
146 123
147 ]]></help> 124 ]]></help>
148 <citations> 125 <expand macro="citations" />
149 <citation type="doi">10.1186/1471-2105-10-168</citation>
150 <citation type="doi">10.1093/nar/gkq383</citation>
151 </citations>
152 </tool> 126 </tool>