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1 <tool id="ctb_remove_protonation_state" name="Remove protonation state" version="0.1">
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2 <description>of every atom</description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" 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 remove_protonation_state.py
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9 -i $infile
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10 -o $outfile
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11 --iformat "${infile.ext}"
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12 2>&1
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13 </command>
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14 <inputs>
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15 <param name="infile" type="data" format="sdf,smi,mol,inchi" label="Molecule file" help="Dataset missing? See TIP below"/>
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16 </inputs>
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17 <outputs>
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18 <data format_source="infile" name="outfile" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 </test>
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23 </tests>
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24 <help>
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25
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26 .. class:: infomark
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27
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28 **What this tool does**
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29
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30 Removes the protonation state of every atom.
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31
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32 -----
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33
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34 .. class:: infomark
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35
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36 **Cite**
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37
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38 `Open Babel`_
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39
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40 .. _Open Babel: http://openbabel.org/wiki/Main_Page
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41
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42 </help>
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43 </tool>
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