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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 63d8775d73dd16e3ee8836ea8c06c81801e87c71
author bgruening
date Mon, 28 Nov 2016 02:08:39 -0500
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bdfd80d7586d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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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 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive">
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9 <![CDATA[
bdfd80d7586d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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10 python $__tool_directory__/remove_protonation_state.py
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11 -i $infile
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12 -o $outfile
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13 --iformat "${infile.ext}"
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14 ]]>
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15 </command>
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16 <inputs>
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17 <expand macro="infile_all_types"/>
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18 </inputs>
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19 <outputs>
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20 <expand macro="output_like_input"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
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25 <output name="outfile" ftype="sdf" file="ob_remove_protonation_state.sdf" lines_diff="2" />
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26 </test>
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27 </tests>
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28 <help>
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29 <![CDATA[
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30
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31 .. class:: infomark
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bdfd80d7586d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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33 **What this tool does**
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35 Removes the protonation state of every atom.
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37 -----
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39 .. class:: infomark
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41 **Cite**
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43 `Open Babel`_
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45 .. _Open Babel: http://openbabel.org/wiki/Main_Page
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47 ]]>
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48 </help>
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49 <expand macro="citations"/>
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50 </tool>