Mercurial > repos > bgruening > enumerate_charges

annotate enumerate_charges.xml @ 1:3d96dc99698f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 09b22cceacb34dd4c6c1b42890f93232df128208"
author bgruening
date Sat, 21 Mar 2020 14:03:09 -0400
parents 0f3e5c69251e
children 36360fa103d6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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1 <tool id="enumerate_charges" name="Enumerate changes" version="0.1">
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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2 <description>calculated with Dimorphite DL and RDKit</description>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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3 <requirements>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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4 <requirement type="package" version="2019.09.2">rdkit</requirement>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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5 </requirements>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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6 <command detect_errors="exit_code">
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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7 <![CDATA[
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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8 python '$__tool_directory__/dimorphite_dl.py'
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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9 --smiles_file '$input'
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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10 --output_file '$output'
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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11 --min_ph $min_ph
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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12 --max_ph $max_ph
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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13 ]]>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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14 </command>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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15 <inputs>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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16 <param name="input" format="smi" type="data" label="Input molecule data"
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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17 help="In SMILES format"/>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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18 <param name="min_ph" type="float" label="Minimum pH" value="6.4" min="0" max="14"/>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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19 <param name="max_ph" type="float" label="Maximum pH" value="8.4" min="0" max="14"/>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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20 </inputs>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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21 <outputs>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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22 <data format="smi" name="output" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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23 </outputs>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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24 <tests>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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25 <test>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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26 <param name="input" ftype='smi' value="mols.smi" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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27 <param name="min_ph" value="6.4" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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28 <param name="max_ph" value="8.4" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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29 <output name="output" ftype='smi'>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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30 <!-- there are problems comparing the output to the expected due to whitespace differences
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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31 so we just check that the number of lines is as expected -->
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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32 <assert_contents>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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33 <has_n_lines n="7" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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34 <has_text text="NC(CCCC[NH3+])C(=O)[O-]" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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35 <has_text text="NCCCCC(N)C(=O)[O-]" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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36 <has_text text="NCCCCC([NH3+])C(=O)[O-]" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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37 </assert_contents>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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38 </output>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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39 </test>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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40 <test>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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41 <param name="input" ftype='smi' value="mols.smi" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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42 <param name="min_ph" value="4.4" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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43 <param name="max_ph" value="10.4" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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44 <output name="output" ftype='smi'>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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45 <assert_contents>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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46 <has_n_lines n="14" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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47 <has_text text="NC(CCCC[NH3+])C(=O)O" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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48 <has_text text="NCCCCC([NH3+])C(=O)[O-]" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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49 <has_text text="NC(CCCC[NH3+])C(=O)[O-]" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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50 <has_text text="NCCCCC([NH3+])C(=O)O" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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51 <has_text text="NC(CCCC[NH3+])C(=O)O" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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52 <has_text text="NCCCCC(N)C(=O)O" />
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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53 </assert_contents>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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54 </output>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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55 </test>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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56 </tests>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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57 <help>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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58 <![CDATA[
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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59
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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60 .. class:: infomark
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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61
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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62 **What this tool does**
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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63
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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64 Dimorphite DL provides rules on how to enumerate the different charge forms of molecules using RDKit.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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65 Source code can be found here: https://git.durrantlab.pitt.edu/jdurrant/dimorphite_dl
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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66
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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67
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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68 -----
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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69
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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70 .. class:: infomark
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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71
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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72 **Input**
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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73
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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74 - `SMILES Format`_
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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75
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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76 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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77
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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78 -----
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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79
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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80 .. class:: infomark
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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81
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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82 **Output**
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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83
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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84 SMILES format with the enumerated molecules. If an ID was provided in the input this is retained in the output.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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85
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86
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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87 ]]>
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88 </help>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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89 <citations>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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90 <citation type="doi">10.1186/s13321-019-0336-9</citation>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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91 <citation type="bibtex">
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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92 @article{rdkit,
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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93 author = {Greg Landrum and others},
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94 title = {RDKit: Open-source cheminformatics},
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95 url ={http://www.rdkit.org}
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96 }</citation>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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97 </citations>
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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98 </tool>