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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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2
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8 <![CDATA[
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9 remove_protonation_state.py
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10 -i $infile
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11 -o $outfile
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12 --iformat "${infile.ext}"
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13 2>&1
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param name="infile" type="data" format="sdf,smi,mol,inchi" label="Molecule file" help="Dataset missing? See TIP below"/>
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18 </inputs>
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19 <outputs>
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20 <data format_source="infile" name="outfile" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 </test>
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25 </tests>
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26 <help>
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2
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27 <![CDATA[
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28
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29 .. class:: infomark
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30
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31 **What this tool does**
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32
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33 Removes the protonation state of every atom.
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34
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35 -----
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36
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37 .. class:: infomark
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38
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39 **Cite**
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40
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41 `Open Babel`_
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42
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43 .. _Open Babel: http://openbabel.org/wiki/Main_Page
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44
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2
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45 ]]>
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46 </help>
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47 </tool>
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