annotate ob_remIons.xml @ 14:4e3b2049a4d3 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
author bgruening
date Tue, 10 Nov 2020 20:32:05 +0000
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1 <tool id="openbabel_remIons" name="Remove counterions and fragments" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>from a library of compounds</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 <token name="@GALAXY_VERSION@">2</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 '$__tool_directory__/ob_remIons.py'
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12 -i '${infile}'
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13 -iformat '${infile.ext}'
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14 -o '${outfile}'
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15 $index
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16 ]]>
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17 </command>
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18 <inputs>
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19 <expand macro="infile_all_types"/>
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20 <param name="index" type="boolean" checked="false" truevalue="-idx" falsevalue="" label="Output indexed tab-separated table?" help="Add an index column to the output file. This option will work only when input format is InChI or SMILES, otherwise it will be ignored." />
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21 </inputs>
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22 <outputs>
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23 <expand macro="output_like_input"/>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="infile" ftype="smi" value="2_mol.smi"/>
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28 <output name="outfile" ftype="smi" file="obrmions_on_2_mol.smi" />
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29 </test>
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30 <test>
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31 <param name="infile" ftype="inchi" value="na-sal.inchi"/>
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32 <output name="outfile" ftype="inchi" file="na-sal_obrmions.inchi" />
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33 </test>
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34 <test>
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35 <param name="infile" ftype="inchi" value="multiple.inchi"/>
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36 <param name="index" value="true"/>
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37 <output name="outfile" ftype="inchi" file="multiple_obrmions.inchi" />
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38 </test>
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39 </tests>
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40 <help>
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41 <![CDATA[
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43 .. class:: infomark
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44
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45 **What this tool does**
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46
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47 Parses a multiple molecules file and deletes any counterions or fragments present.
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49 -----
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50
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51 .. class:: warningmark
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52
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53 **Hint**
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54
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55 | For each molecule, all fragments except for the largest are deleted.
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56 |
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57 | Only molecules with more than 5 heavy atoms are parsed.
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58
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59
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60 ]]>
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61 </help>
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62 <expand macro="citations"/>
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63 </tool>