Mercurial > repos > recetox > filter_compounds

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit b757d35278216a1f43bd53ea687a951b005e47df
author recetox
date Wed, 20 Mar 2024 12:20:17 +0000
parents 72b687d21f65
children
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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1 <tool id="filter_orgmet_anorg" name="Filter organometallics and/or anorganics" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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2 <description>from a library of compounds</description>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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3 <macros>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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4 <import>macros.xml</import>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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5 </macros>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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6 <expand macro="creator"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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7 <expand macro="requirements"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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8 <command detect_errors="aggressive">
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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9 <![CDATA[
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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10 python '$__tool_directory__/filter_compounds.py'
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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11 -i '${infile}'
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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12 -o '${outfile}'
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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13 $metorg
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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14 $anorg
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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15 ]]>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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16 </command>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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17 <inputs>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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18 <param name="infile" type="data" format="smi" label="Select input file"
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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19 help="Currently only SMILES identifiers are allowed as an input."/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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20 <param name="metorg" type="boolean" checked="false" truevalue="-m" falsevalue=""
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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21 label="Filter out organometallic compounds?"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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22 <param name="anorg" type="boolean" checked="false" truevalue="-a" falsevalue=""
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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23 label="Filter out anorganic compounds?"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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24 </inputs>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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25 <outputs>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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26 <data format="smi" name="outfile"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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27 </outputs>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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28 <tests>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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29 <test>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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30 <param name="infile" ftype="smi" value="input_all.smi"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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31 <param name="metorg" value="true"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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32 <param name="anorg" value="true"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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33 <output name="outfile" ftype="smi" file="output_all.smi"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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34 </test>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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35 <test>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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36 <param name="infile" ftype="smi" value="input_all_table.smi"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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37 <param name="metorg" value="true"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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38 <param name="anorg" value="true"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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39 <output name="outfile" ftype="smi" file="output_all_table.smi"/>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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40 </test>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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41 </tests>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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42 <help>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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43 <![CDATA[
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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44 @HELP@
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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45 ]]>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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46 </help>
1
6c5df3eeb768 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit b757d35278216a1f43bd53ea687a951b005e47df
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47 <citations>
6c5df3eeb768 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit b757d35278216a1f43bd53ea687a951b005e47df
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48 <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
6c5df3eeb768 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit b757d35278216a1f43bd53ea687a951b005e47df
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49 </citations>
0
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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50 </tool>
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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51