Mercurial > repos > bgruening > sdf_to_tab
annotate sdf_to_tab.xml @ 0:06828e0cc8a7 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
author | bgruening |
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date | Wed, 16 Oct 2019 07:26:19 -0400 |
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children | 40ff81f67f5e |
rev | line source |
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0
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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1 <tool id="sdf_to_tab" name="Extract values from an SD-file" version="@VERSION@"> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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2 <macros> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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3 <token name="@VERSION@">2019.03.1</token> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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4 </macros> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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5 <description>into a tabular file using RDKit</description> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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6 <requirements> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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7 <requirement type="package" version="@VERSION@">rdkit</requirement> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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8 </requirements> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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9 <command detect_errors="exit_code"> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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10 <![CDATA[ |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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11 python '$__tool_directory__/sdf_to_tab.py' |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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12 -i '${infile}' |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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13 -o '${outfile}' |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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14 -p '$props' |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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15 $header |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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16 $smiles |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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17 $name |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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18 ]]> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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19 </command> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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changeset
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20 <inputs> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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21 <param name="infile" format="sdf" type="data" label="Input SD-file"/> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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22 <param name="header" type="boolean" label="Include the property name as header" |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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23 truevalue="--header" falsevalue="" checked="false" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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24 <param name="smiles" type="boolean" label="Include SMILES as column in output" |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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25 truevalue="--smiles" falsevalue="" checked="false" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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26 <param name="name" type="boolean" label="Include molecule name as column in output" |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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27 truevalue="--name" falsevalue="" checked="false" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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28 <param name="props" type="text" optional="true" label="Properties to extract from the SD-file" help="Separated with a comma, e.g. RMSD_UB,RMSD_LB,SCORE. To extract values for all properties in the file, leave the field blank."/> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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29 </inputs> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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30 <outputs> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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31 <data format="tabular" name="outfile" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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32 </outputs> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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33 <tests> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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34 <test> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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35 <param name="infile" ftype='sdf' value="CID_3037.sdf" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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36 <param name="header" value="True" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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37 <param name="props" value="" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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38 <param name="name" value="True" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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39 <output name="outfile" ftype='tabular' file="CID_3037.tab" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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40 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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41 </test> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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42 <test> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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43 <param name="infile" ftype='sdf' value="ligand.sdf" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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44 <param name="header" value="True" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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45 <param name="props" value="RMSD_UB,RMSD_LB,SCORE" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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46 <param name="smiles" value="True" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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47 <output name="outfile" ftype='tabular' file="ligand.tab" /> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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48 </test> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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49 </tests> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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50 <help> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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51 <![CDATA[ |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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52 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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53 .. class:: infomark |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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54 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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55 **What this tool does** |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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56 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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57 Structure-data (SD-) files may contain values for various properties saved under each of the records. These are indicated using angled brackets, as in the following extract:: |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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58 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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59 > <TORSDO> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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60 F 3 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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61 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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62 > <SCORE> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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63 -4.9 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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64 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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65 > <RMSD_LB> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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66 0.000 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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67 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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68 > <RMSD_UB> |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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69 0.000 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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70 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
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71 This tool extracts properties for all molecules saved within an input SD-file, using RDKit, and saves them to tabular format. |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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72 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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73 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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74 ----- |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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75 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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76 .. class:: infomark |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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77 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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78 **Input** |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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79 |
06828e0cc8a7
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
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80 An SD-file. The properties to be extracted can also be specified, separated with a comma; for example, SCORE,RMSD_LB,RMSD_UB. |
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81 |
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82 If the field is left blank, all properties found in the SD-file will be saved, excluding properties with values that contain newline or tab characters, which would disrupt the tabular format. |
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83 |
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84 ----- |
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85 |
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86 .. class:: infomark |
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87 |
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88 **Output** |
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89 |
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90 Tabular file, where each property is shown in a separate column, with compounds found in the SD-file listed in each row:: |
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91 |
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92 Name RMSD_LB RMSD_UB SCORE |
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93 pose1 0.0 0.0 -4.9 |
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94 pose2 0.118 2.246 -4.9 |
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95 pose3 2.96 5.795 -4.9 |
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96 pose4 2.958 5.379 -4.8 |
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97 pose5 2.763 5.379 -4.5 |
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98 pose6 3.106 4.85 -4.4 |
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99 pose7 2.847 5.816 -4.4 |
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100 pose8 3.964 5.892 -4.3 |
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101 pose9 3.971 6.363 -4.3 |
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102 |
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103 ]]> |
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104 </help> |
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105 <citations> |
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106 <citation type="bibtex"> |
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107 @article{rdkit, |
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108 author = {Greg Landrum and others}, |
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109 title = {RDKit: Open-source cheminformatics}, |
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110 url ={http://www.rdkit.org} |
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111 }</citation> |
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112 </citations> |
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113 </tool> |