Mercurial > repos > bgruening > openbabel_remove_protonation_state

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 10:53:50 +0000
parents ad98596cf471
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e946a539ddf7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="openbabel_remove_protonation_state" name="Remove protonation state" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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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 <token name="@GALAXY_VERSION@">1</token>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive">
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10 <![CDATA[
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11 python '$__tool_directory__/remove_protonation_state.py'
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12 -i '$infile'
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13 -o '$outfile'
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14 --iformat '${infile.ext}'
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15 ]]>
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16 </command>
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17 <inputs>
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18 <expand macro="infile_all_types"/>
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19 </inputs>
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20 <outputs>
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21 <expand macro="output_like_input"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
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26 <output name="outfile" ftype="sdf" file="ob_remove_protonation_state.sdf" lines_diff="2" />
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27 </test>
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28 <test>
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29 <param name="infile" ftype="inchi" value="na-sal.inchi"/>
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30 <output name="outfile" ftype="inchi" file="ob_remove_protonation_state.inchi" />
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31 </test>
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32 </tests>
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33 <help>
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34 <![CDATA[
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36 .. class:: infomark
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38 **What this tool does**
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40 Removes the protonation state of every atom.
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44 ]]>
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45 </help>
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46 <expand macro="citations"/>
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47 </tool>