annotate select_points_SDF.xml @ 2:7255688c77f3 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:44:17 -0400
parents 8e214e52e461
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1 <tool id="ctb_frankenstein_ligand" name="Create Frankenstein ligand" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>for docking active site definition</description>
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3 <macros>
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4 <import>rdock_macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
0
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7 <requirements>
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8 <requirement type="package" version="3.7">python</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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11 python '$__tool_directory__/select_points_SDF.py'
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12 -i '$infile'
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13 -o '$outfile'
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14 ]]></command>
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15 <inputs>
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16 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
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17 </inputs>
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18 <outputs>
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19 <data name="outfile" format="sdf"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="infile" value="input.sdf" ftype="sdf"/>
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24 <output name="outfile" ftype='sdf' file="select_points_output.sdf"/>
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25 </test>
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26 <test>
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27 <param name="infile" value="input_v3000.sdf" ftype="sdf"/>
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28 <output name="outfile" ftype='sdf' file="select_points_output_v3000.sdf"/>
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29 </test>
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30 </tests>
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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31 <help><![CDATA[
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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32
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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33 .. class:: infomark
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34
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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35 **What it does**
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36
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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37 Converts an SD file containing multiple molecules into a 'Frankenstein ligand' with a 3D shape combining all ligands, which can be used for definition of an active site with rDock.
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38
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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39 This tool is based on a Perl script originally written by Peter Schmidtke.
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40
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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41 _____
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42
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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43 .. class:: infomark
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44
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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45 **Input**
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46
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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47 - SD file containing multiple molecules.
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48
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49 _____
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50
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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51 .. class:: infomark
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52
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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53 **Output**
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54
7a4306d69801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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55 - SD file containing the 'Frankenstein ligand'.
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56 ]]></help>
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57 <citations>
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58 <citation type="doi">10.1371/journal.pcbi.1003571</citation>
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59 <citation type="bibtex">
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60 @article{rdock,
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61 author = {Peter Schmidtke},
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62 title = {'Select points' script for generation of a Frankenstein ligand},
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63 url = {https://github.com/InformaticsMatters/docking-validation/blob/master/scripts/select_points_SDF.pl}
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64 }</citation>
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65 </citations>
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66 </tool>