Mercurial > repos > bgruening > fpocket

annotate fpocket.xml @ 2:4fb73be7f4cb draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:29:23 -0400
parents 909c8763f127
children 4cc9d85c3bae
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4fb73be7f4cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="fpocket" name="fpocket" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
4fb73be7f4cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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2 <macros>
4fb73be7f4cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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3 <token name="@TOOL_VERSION@">3.1.4.2</token>
4fb73be7f4cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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4 <token name="@GALAXY_VERSION@">0</token>
4fb73be7f4cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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5 </macros>
0
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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6 <description>- find potential binding sites in protein structures</description>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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7 <requirements>
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4fb73be7f4cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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8 <requirement type="package" version="@TOOL_VERSION@">fpocket</requirement>
0
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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9 </requirements>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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10 <command detect_errors="exit_code"><![CDATA[
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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11
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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12 ln -s '$input' ./input.pdb &&
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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13 fpocket
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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14 -f ./input.pdb
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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15 #if $inp.pocket_type == 'channel':
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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16 -m 2.8 -M 5.5 -i 30
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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17 #elif $inp.pocket_type == 'external':
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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18 -m 3.5 -M 10 -i 30
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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19 #elif $inp.pocket_type == 'custom':
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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20 -m $inp.min -M $inp.max -i $inp.i -D $inp.D -C $inp.C -e $inp.e
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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21 #end if
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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22
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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23 ]]></command>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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24 <inputs>
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25 <param name="input" type="data" format="pdb" label="Input file" help="Protein structure file (PDB) to search."/>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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26 <conditional name="inp">
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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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">
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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28 <option value="small_mol">Small molecule binding sites</option>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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29 <option value="channel">Putative channels and small cavities</option>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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30 <option value="external">Large, external pockets</option>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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31 <option value="custom">Custom options (advanced)</option>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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32 </param>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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33 <when value="custom">
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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."/>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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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."/>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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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"/>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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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"/>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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38 <param name="C" type="select" value="s" label="Clustering method for grouping Voronoi vertices" help="Method for clustering alpha spheres">
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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39 <option value="s">Single linkage clustering</option>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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40 <option value="m">Complete linkage clustering</option>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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41 <option value="a">Average linkage clustering</option>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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42 <option value="c">Centroid linkage clustering</option>
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43 </param>
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44 <param name="e" type="select" value="e" label="Distance measure for clustering">
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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45 <option value="e">Euclidean distance</option>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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46 <option value="b">Manhattan distance</option>
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47 </param>
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48 </when>
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49 <when value="small_mol"/>
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50 <when value="channel"/>
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51 <when value="external"/>
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52 </conditional>
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53 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files">
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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54 <option value="atoms" selected="true">PDB files containing the atoms in contact with each pocket</option>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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55 <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option>
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56 <option value="alpha_pdb" selected="true">PDB file containing alpha spheres found</option>
909c8763f127 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 51f8b6831c513a56bac5aae0d06c936ad6fa8ea8"
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57 <option value="all_verts" selected="true">PQR file containing all Voronoi vertices found</option>
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58 <option value="info" selected="true">Log file containing pocket properties</option>
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59 </param>
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60 </inputs>
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61
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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62 <outputs>
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63 <collection type="list" name="atoms_output" label="Atoms in contact with each pocket">
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64 <discover_datasets pattern="(?P&lt;designation&gt;^pocket\d+)_atm\.pdb$" directory="input_out/pockets" ext="pdb"/>
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65 <filter>"atoms" in outputs</filter>
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66 </collection>
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67 <collection type="list" name="pock_verts_output" label="Voronoi vertices of each pocket">
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68 <discover_datasets pattern="(?P&lt;designation&gt;^pocket\d+)_vert\.pqr$" directory="input_out/pockets" ext="pqr"/>
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69 <filter>"pock_verts" in outputs</filter>
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70 </collection>
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71 <data format="pqr" name="all_verts_output" label="All Voronoi vertices found" from_work_dir="input_out/input_pockets.pqr">
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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72 <filter>"all_verts" in outputs</filter>
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73 </data>
1
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74 <data format="pdb" name="alpha_pdb_output" label="PDB output with alpha spheres" from_work_dir="input_out/input_out.pdb">
909c8763f127 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 51f8b6831c513a56bac5aae0d06c936ad6fa8ea8"
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75 <filter>"alpha_pdb" in outputs</filter>
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76 </data>
0
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77 <data format="txt" name="info_output" label="Pocket properties" from_work_dir="input_out/input_info.txt">
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78 <filter>"info" in outputs</filter>
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79 </data>
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80 </outputs>
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81
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82 <tests>
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83 <!-- lines_diff needed because volume estimates are calculated via a Monte Carlo method and vary with each run -->
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84 <test>
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85 <param name="input" ftype="pdb" value="2brc.pdb"/>
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86 <param name='pocket_type' value='custom' />
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87 <param name="min" value="4.0"/>
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88 <param name="max" value="7.0"/>
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89 <param name="i" value="20" />
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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90 <param name="D" value="2.0"/>
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91 <param name="C" value="c" />
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92 <param name="e" value="b" />
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93 <param name='outputs' value='pock_verts,all_verts' />
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94 <output_collection name="pock_verts_output" type="list">
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95 <element name="pocket2" ftype="pqr" file="pocket2_vert.pqr" lines_diff="2"/>
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96 </output_collection>
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97 <output name="all_verts_output" ftype="pqr" file='custom_pockets.pqr'/>
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98 </test>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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99 <test>
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100 <param name="input" ftype="pdb" value="2brc.pdb"/>
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101 <param name='pocket_type' value='small_mol' />
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102 <output_collection name="atoms_output" type="list">
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103 <element name="pocket1" ftype="pdb" file="pocket1_atm.pdb" lines_diff="2"/>
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104 </output_collection>
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105 <output name="info_output" ftype="txt" file='2brc_info.txt' lines_diff="20"/>
1
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106 <output name="alpha_pdb_output" ftype="pdb">
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107 <assert_contents>
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108 <has_text text="ATOM 1 N MET A 1"/>
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109 <has_text text="HETATM 6 APOL STP C "/>
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110 </assert_contents>
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111 </output>
0
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112 </test>
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113 </tests>
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114 <help><![CDATA[
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115
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116 Detect 'pockets' in a protein structure using the fpocket software. A potential use
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117 of this tool is locating potential binding sites in a protein prior to performing
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118 protein-ligand docking.
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119
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120 To use, upload a protein structure in PDB format and select the type of pocket to
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121 detect. 'Custom options' can also be selected - this exposes all internal fpocket
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122 parameters. Using this option requires some knowledge of the fpocket prediction
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123 algorithm. Please consult the cited publications for more details.
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124
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125
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126 -----
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127
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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128 .. class:: infomark
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129
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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130 **Input**
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131
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132 A protein structure in PDB format.
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133
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134 -----
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135
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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136 .. class:: infomark
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137
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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138 **Output**
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139
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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140 Some or all of the following files:
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141
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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142 - A collection of PDB files, one for each pocket, each containing the atoms bordering the pocket.
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143 - A collection of PQR files, one for each pocket, each containing Voronoi vertices of the pocket.
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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144 - A single PQR file containing all Voronoi vertices for all pockets.
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145 - A text file listing properties of all pockets detected.
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146
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147 ]]></help>
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148 <citations>
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149 <citation type="doi">10.1186/1471-2105-10-168</citation>
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150 <citation type="doi">10.1093/nar/gkq383</citation>
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151 </citations>
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152 </tool>