Mercurial > repos > bgruening > ctb_frankenstein_ligand

annotate select_points_SDF.xml @ 0:355c1759835c draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
author bgruening
date Mon, 04 May 2020 11:39:06 +0000
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children 2c6653fb7ad2
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355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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1 <tool id="ctb_frankenstein_ligand" name="Create Frankenstein ligand" version="0.1.0">
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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2 <description>for docking active site definition</description>
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3 <requirements>
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4 <requirement type="package" version="3.7">python</requirement>
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5 </requirements>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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6 <command detect_errors="exit_code"><![CDATA[
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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7 python '$__tool_directory__/select_points_SDF.py'
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8 -i '$infile'
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9 -o '$outfile'
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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10 ]]></command>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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11 <inputs>
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12 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
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13 </inputs>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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14 <outputs>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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15 <data name="outfile" format="sdf"/>
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16 </outputs>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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17 <tests>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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18 <test>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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19 <param name="infile" value="input.sdf" ftype="sdf"/>
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20 <output name="outfile" ftype='sdf' file="select_points_output.sdf"/>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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21 </test>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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22 <test>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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23 <param name="infile" value="input_v3000.sdf" ftype="sdf"/>
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24 <output name="outfile" ftype='sdf' file="select_points_output_v3000.sdf"/>
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25 </test>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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26 </tests>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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27 <help><![CDATA[
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28
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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29 .. class:: infomark
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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30
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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31 **What it does**
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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32
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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33 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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34
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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35 This tool is based on a Perl script originally written by Peter Schmidtke.
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36
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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37 _____
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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38
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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39 .. class:: infomark
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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40
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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41 **Input**
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42
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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43 - SD file containing multiple molecules.
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44
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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45 _____
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46
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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47 .. class:: infomark
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48
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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49 **Output**
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50
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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51 - SD file containing the 'Frankenstein ligand'.
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52 ]]></help>
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53 <citations>
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54 <citation type="doi">10.1371/journal.pcbi.1003571</citation>
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55 <citation type="bibtex">
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56 @article{rdock,
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57 author = {Peter Schmidtke},
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58 title = {'Select points' script for generation of a Frankenstein ligand},
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59 url = {https://github.com/InformaticsMatters/docking-validation/blob/master/scripts/select_points_SDF.pl}
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60 }</citation>
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61 </citations>
355c1759835c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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62 </tool>