annotate ob_remIons.xml @ 2:bf3b0107c0f4 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 78ac0521d7df684e96c1b9c1ba2a17b02e681608
author bgruening
date Sat, 20 May 2017 20:03:56 -0400
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children 04da8dc033e1
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c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 <tool id="openbabel_remIons" name="Remove counterions and fragments" version="@VERSION@.0">
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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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 <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">
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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9 <![CDATA[
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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10 python '$__tool_directory__/ob_remIons.py'
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11 -i '${infile}'
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12 -iformat '${infile.ext}'
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13 -o '${outfile}'
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14 ]]>
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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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="smi" value="2_mol.smi"/>
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25 <output name="outfile" ftype="smi" file="obrmions_on_2_mol.smi" />
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26 </test>
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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27 </tests>
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28 <help>
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29 <![CDATA[
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30
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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31 .. class:: infomark
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32
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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33 **What this tool does**
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34
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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35 Parses a multiple molecules file and deletes any present counterions or fragments.
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36
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37 -----
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38
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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39 .. class:: warningmark
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40
c9bee3591df9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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41 **Hint**
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42
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43 | Only the **largest fragment** on every molecule is extracted.
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44 |
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45 | Only molecules with more than 5 heavy atoms are parsed.
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46
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47
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48 ]]>
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49 </help>
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50 <expand macro="citations"/>
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51 </tool>