Mercurial > repos > iuc > humann_join_tables

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit cb7dc8ff1810f6d335b5dd6615651f32a3ea7447
author iuc
date Fri, 27 Sep 2024 09:54:53 +0000
parents 9d9297da2d7e
children
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9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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1 <tool id="humann_join_tables" name="Join (merge)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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2 <description>gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single table</description>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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3 <macros>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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4 <import>macros.xml</import>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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5 </macros>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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6 <expand macro="edam_ontology"/>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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7 <expand macro="requirements"/>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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8 <expand macro="version"/>
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9 <command detect_errors="exit_code"><![CDATA[
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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10 #import re
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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11 mkdir tmp_dir
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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12 &&
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13 #for $input in $inputs
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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14 ln -s '$input' 'tmp_dir/${re.sub('[^\w\-_.]', '_', input.element_identifier)}' &&
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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15 #end for
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16 humann_join_tables
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17 -i 'tmp_dir'
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18 -o '$output'
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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19 ]]></command>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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20 <inputs>
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21 <param name="inputs" type="data" format="tsv,tabular" multiple="true" label="Gene/pathway table"/>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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22 </inputs>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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23 <outputs>
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24 <data format="tabular" name="output"/>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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25 </outputs>
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26 <tests>
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27 <test expect_num_outputs="1">
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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28 <param name="inputs" value="demo_pathabundance.tsv,demo_pathcoverage.tsv"/>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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29 <output name="output" ftype="tabular" value="demo_joined_pathabundance_pathcoverage.tsv">
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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30 <assert_contents>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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31 <has_text text="humann_Abundance" />
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32 <has_text text="humann_Coverage" />
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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33 <has_text text="UNINTEGRATED|unclassified" />
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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34 <has_text text="PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified" />
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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35 </assert_contents>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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36 </output>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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37 </test>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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38 </tests>
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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39 <help><![CDATA[
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40 @HELP_HEADER@
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41
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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42 This tool joins (merges) multiple single-sample output files into a single table with multiple samples.
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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43 It can also be used to join multiple multi-sample output files into a single table.
9d9297da2d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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44 ]]></help>
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45 <expand macro="citations"/>
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46 </tool>