Mercurial > repos > recetox > filter_compounds

annotate filter_compounds.xml @ 1:686850eb1e64 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:21:21 +0000
parents 987357c6941c
children 8eb6e392c92b
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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-->
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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4 <macros>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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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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686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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8 <expand macro="creator"/>
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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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9 <expand macro="requirements"/>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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10 <command detect_errors="aggressive">
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686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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11 <![CDATA[
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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12 python '$__tool_directory__/filter_compounds.py'
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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13 -i '${infile}'
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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14 -o '${outfile}'
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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15 $metorg
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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16 $anorg
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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17 ]]>
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18 </command>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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19 <inputs>
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686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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20 <param name="infile" type="data" format="smi" label="Select input file"
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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21 help="Currently only SMILES identifiers are allowed as an input."/>
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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22 <param name="metorg" type="boolean" checked="false" truevalue="-m" falsevalue=""
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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23 label="Filter out organometallic compounds?"/>
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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24 <param name="anorg" type="boolean" checked="false" truevalue="-a" falsevalue=""
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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25 label="Filter out anorganic compounds?"/>
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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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26 </inputs>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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27 <outputs>
1
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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28 <data format="smi" name="outfile"/>
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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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29 </outputs>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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30 <tests>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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31 <test>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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32 <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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33 <param name="metorg" value="true"/>
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686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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34 <param name="anorg" value="true"/>
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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35 <output name="outfile" ftype="smi" file="output_all.smi"/>
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36 </test>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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37 <test>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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38 <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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39 <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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40 <param name="anorg" value="true"/>
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41 <output name="outfile" ftype="smi" file="output_all_table.smi"/>
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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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42 </test>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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43 </tests>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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44 <help>
1
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45 <![CDATA[
686850eb1e64 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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46 @HELP@
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47 ]]>
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48 </help>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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49 </tool>
987357c6941c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
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