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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
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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@">
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4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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2 <description>- find potential binding sites in protein structures</description>
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4fb73be7f4cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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3 <macros>
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4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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4 <import>macros.xml</import>
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4fb73be7f4cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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5 <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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6 </macros>
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4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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7 <expand macro="requirements" />
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8 <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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2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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10 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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11 fpocket
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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12 -f ./input.pdb
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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13 #if $inp.pocket_type == 'channel':
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4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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14 --min_alpha_size 2.8 --max_alpha_size 5.5 --min_spheres_per_pocket 30
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15 #elif $inp.pocket_type == 'external':
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4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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16 --min_alpha_size 3.5 --max_alpha_size 10 --min_spheres_per_pocket 30
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17 #elif $inp.pocket_type == 'custom':
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4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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18 --min_alpha_size $inp.min
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19 --max_alpha_size $inp.max
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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20 --min_spheres_per_pocket $inp.i
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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21 --clustering_distance $inp.D
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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22 --clustering_method $inp.C
4cc9d85c3bae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 06eccf2513b3394e79606f320e019be4793386b9"
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23 --clustering_measure $inp.e
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24 #end if
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2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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26 ]]></command>
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27 <inputs>
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28 <param name="input" type="data" format="pdb" label="Input file" help="Protein structure file (PDB) to search."/>
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29 <expand macro="inputs" />
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30 <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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31 <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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32 <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option>
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33 <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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34 <option value="all_verts" selected="true">PQR file containing all Voronoi vertices found</option>
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35 <option value="info" selected="true">Log file containing pocket properties</option>
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36 </param>
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37 </inputs>
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38
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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39 <outputs>
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40 <collection type="list" name="atoms_output" label="Atoms in contact with each pocket">
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41 <discover_datasets pattern="(?P&lt;designation&gt;^pocket\d+)_atm\.pdb$" directory="input_out/pockets" ext="pdb"/>
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42 <filter>"atoms" in outputs</filter>
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43 </collection>
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44 <collection type="list" name="pock_verts_output" label="Voronoi vertices of each pocket">
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45 <discover_datasets pattern="(?P&lt;designation&gt;^pocket\d+)_vert\.pqr$" directory="input_out/pockets" ext="pqr"/>
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46 <filter>"pock_verts" in outputs</filter>
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47 </collection>
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48 <data format="pqr" name="all_verts_output" label="All Voronoi vertices found" from_work_dir="input_out/input_pockets.pqr">
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49 <filter>"all_verts" in outputs</filter>
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50 </data>
1
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51 <data format="pdb" name="alpha_pdb_output" label="PDB output with alpha spheres" from_work_dir="input_out/input_out.pdb">
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52 <filter>"alpha_pdb" in outputs</filter>
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53 </data>
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54 <data format="txt" name="info_output" label="Pocket properties" from_work_dir="input_out/input_info.txt">
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55 <filter>"info" in outputs</filter>
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56 </data>
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57 </outputs>
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58
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59 <tests>
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60 <!-- lines_diff needed because volume estimates are calculated via a Monte Carlo method and vary with each run -->
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61 <test>
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62 <param name="input" ftype="pdb" value="2brc.pdb"/>
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63 <param name='pocket_type' value='custom' />
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64 <param name="min" value="1.0"/>
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65 <param name="max" value="3.0"/>
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66 <param name="i" value="20" />
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67 <param name="D" value="2.0"/>
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68 <param name="C" value="c" />
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69 <param name="e" value="b" />
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70 <param name='outputs' value='pock_verts,all_verts' />
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71 <output_collection name="pock_verts_output" type="list">
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72 <element name="pocket2" ftype="pqr" file="pocket2_vert.pqr" lines_diff="2"/>
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73 </output_collection>
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74 <output name="all_verts_output" ftype="pqr" file='custom_pockets.pqr'/>
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75 </test>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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76 <test>
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77 <param name="input" ftype="pdb" value="2brc.pdb"/>
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78 <param name='pocket_type' value='small_mol' />
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79 <output_collection name="atoms_output" type="list">
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80 <element name="pocket1" ftype="pdb" file="pocket1_atm.pdb" lines_diff="2"/>
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81 </output_collection>
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82 <output name="info_output" ftype="txt" file='2brc_info.txt' lines_diff="20"/>
1
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83 <output name="alpha_pdb_output" ftype="pdb">
909c8763f127 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 51f8b6831c513a56bac5aae0d06c936ad6fa8ea8"
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84 <assert_contents>
909c8763f127 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 51f8b6831c513a56bac5aae0d06c936ad6fa8ea8"
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85 <has_text text="ATOM 1 N MET A 1"/>
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86 <has_text text="HETATM 6 APOL STP C "/>
909c8763f127 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 51f8b6831c513a56bac5aae0d06c936ad6fa8ea8"
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87 </assert_contents>
909c8763f127 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 51f8b6831c513a56bac5aae0d06c936ad6fa8ea8"
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88 </output>
0
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89 </test>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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90 </tests>
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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91 <help><![CDATA[
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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92
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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93 Detect 'pockets' in a protein structure using the fpocket software. A potential use
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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94 of this tool is locating potential binding sites in a protein prior to performing
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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95 protein-ligand docking.
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96
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97 To use, upload a protein structure in PDB format and select the type of pocket to
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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98 detect. 'Custom options' can also be selected - this exposes all internal fpocket
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99 parameters. Using this option requires some knowledge of the fpocket prediction
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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100 algorithm. Please consult the cited publications for more details.
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101
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102
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103 -----
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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104
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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105 .. class:: infomark
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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106
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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107 **Input**
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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108
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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109 A protein structure in PDB format.
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110
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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111 -----
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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112
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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113 .. class:: infomark
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114
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115 **Output**
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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116
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117 Some or all of the following files:
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118
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119 - A collection of PDB files, one for each pocket, each containing the atoms bordering the pocket.
2063e965531c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 3fd527d39458527d9ab82562db2d3d6af29f7f51"
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120 - 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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121 - A single PQR file containing all Voronoi vertices for all pockets.
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122 - A text file listing properties of all pockets detected.
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123
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124 ]]></help>
3
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125 <expand macro="citations" />
0
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126 </tool>