annotate distance_finder.xml @ 0:c066b5accacf draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"
author bgruening
date Wed, 25 Mar 2020 16:47:13 -0400
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1 <tool id="openbabel_structure_distance_finder" name="Determine distance to defined points" version="0.1.0">
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2 <description>- determine the minimum distances between a molecule and a set of 3D points</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <!-- does not run with obabel 2.4.1 -->
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8 <requirement type="package" version="3.0.0">openbabel</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 python '$__tool_directory__/distance_finder.py'
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12 -i '$input'
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13 -p $points_file
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14 -o '$output'
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15 ]]></command>
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16
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17 <configfiles>
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18 <configfile name="points_file">$points</configfile>
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19 </configfiles>
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20
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21 <inputs>
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22 <param type="data" name="input" format="sdf" label="Ligands to be analysed" help="Input in SDF format" />
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23 <param type="text" name="points" area="true" label="3D points to consider" help="Points as X, Y, Z coordinates, one point per line">
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24 <sanitizer invalid_char="">
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25 <valid initial="string.printable">
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26 <remove value="&apos;" />
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27 </valid>
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28 </sanitizer>
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29 </param>
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30 </inputs>
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31 <outputs>
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32 <data format="sdf" name="output" label="The measured ligands"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" ftype="sdf" value="ligands.sdf"/>
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37 <!-- TODO - work out how to specify multi-line text -->
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38 <param name="points" value="5.655 1.497 18.223" />
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39 <output name="output" ftype="sdf">
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40 <assert_contents>
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41 <has_text text="distance1" />
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42 </assert_contents>
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43 </output>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47 .. class:: infomark
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48
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49 **What it does**
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50
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51 This tool reports distances of ligands to reference points provided as atoms in a PDB file.
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52 It is useful for finding out to what extent a ligand occupies an active site.
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53
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54 .. class:: infomark
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55
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56 **Input**
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57
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58 An SD-file containing 3D molecules.
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59
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60 The points parameter contains the points to compare to as X, Y and Z coordinates, one point per line.
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61 An example is:
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62
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63 5.655 1.497 18.223
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64 1.494 -8.367 18.574
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65 13.034 6.306 25.232
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66
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67 This would encode 3 points.
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68
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69 Each record in the SDF input is read and the closest heavy atom to each of the points is recorded as
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70 properties in the output SDF.
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71
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72 .. class:: infomark
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73
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74 **Output**
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75
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76 The same SD file as the input but with a series of "distance?" properties added where ? is the index of the points
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77 being compared to. In the example there would be properties for distance1, distance2 and distance3.
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78
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79
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80 ]]></help>
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81 <expand macro="citations"/>
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82 </tool>
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83