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annotate filter/ob_remIons.xml @ 22:b4ba90dcfde0 default tip

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Tue, 23 Jul 2013 19:00:18 +0200
parents 3d3e7c1d0f49
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1 <tool id="ctb_remIons" name="Remove counterions and fragments" version="1.0">
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2 <description></description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8 ob_remIons.py
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9 -i "${infile}"
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10 -iformat "${infile.ext}"
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11 -o "${outfile}"
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12 </command>
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13 <inputs>
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14 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Select input file with multiple molecules"/>
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15 </inputs>
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16 <outputs>
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17 <data format_source="infile" name="outfile"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="infile" ftype="smi" value="2_mol.smi"/>
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22 <output name="outfile" ftype="smi" file="obrmions_on_2_mol.smi" />
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23 </test>
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24 </tests>
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25 <help>
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26
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27 .. class:: infomark
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28
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29 **What this tool does**
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30
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31 Parses a multiple molecules file and deletes any present counterions or fragments.
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32
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33 -----
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35 .. class:: warningmark
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36
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37 **Hint**
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38
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39 | Only the **largest fragment** on every molecule is extracted.
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40 |
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41 | Only molecules with more than 5 heavy atoms are parsed.
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43 -----
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45 .. class:: infomark
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47 **Cite**
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48
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49 N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
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50
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51 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://journal.chemistrycentral.com/content/2/1/5
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53 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_
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54
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55 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
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57 `Open Babel`_
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58
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59 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
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61 </help>
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62 </tool>