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annotate filter_compounds.xml @ 0:987357c6941c draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
author recetox
date Thu, 07 Jan 2021 11:30:13 +0000
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children 686850eb1e64
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987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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1 <tool id="filter_orgmet_anorg" name="Filter organometallics and/or anorganics" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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2 <description>from a library of compounds</description>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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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>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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6 <token name="@GALAXY_VERSION@">0</token>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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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[
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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11 python '$__tool_directory__/filter_compounds.py'
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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12 -i '${infile}'
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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13 -o '${outfile}'
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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14 $metorg
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15 $anorg
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param name="infile" type="data" format="smi" label="Select input file" help="Currently only SMILES identifiers are allowed as an input."/>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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20 <param name="metorg" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Filter out organometallic compounds?" />
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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21 <param name="anorg" type="boolean" checked="false" truevalue="-a" falsevalue="" label="Filter out anorganic compounds?" />
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22 </inputs>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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23 <outputs>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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24 <data format="smi" name="outfile"/>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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25 </outputs>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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26 <tests>
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27 <test>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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28 <param name="infile" ftype="smi" value="input_all.smi"/>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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29 <param name="metorg" value="true"/>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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30 <param name="anorg" value="true"/>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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31 <output name="outfile" ftype="smi" file="output_all.smi" />
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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32 </test>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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33 <test>
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34 <param name="infile" ftype="smi" value="input_all_table.smi"/>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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35 <param name="metorg" value="true"/>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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36 <param name="anorg" value="true"/>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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37 <output name="outfile" ftype="smi" file="output_all_table.smi" />
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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38 </test>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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39 </tests>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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40 <help>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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41 <![CDATA[
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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43 .. class:: infomark
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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45 **What this tool does**
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46
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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47 Filters organometallics (compounds containing atoms other than C|N|O|P|F|S|I|B|Si|Se|Cl|Br|Li|Na|H|K) or anorganics (compounds without C). Input can be either list of SMILES identifiers or indexed table of SMILES (two tab-separated columns, first column is index, second columns is SMILES).
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48
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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49 ]]>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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50 </help>
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51 </tool>
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52