Mercurial > repos > iuc > humann_reduce_table

annotate humann_reduce_table.xml @ 2:d122106c317f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
author iuc
date Tue, 07 Feb 2023 19:49:34 +0000
parents c2488dbc8e39
children
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c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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1 <tool id="humann_reduce_table" name="Reduce" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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2 <description>a joined HUMAnN table</description>
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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3 <macros>
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4 <import>macros.xml</import>
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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5 </macros>
c2488dbc8e39 "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"/>
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7 <expand macro="requirements"/>
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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8 <expand macro="version"/>
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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9 <command detect_errors="exit_code"><![CDATA[
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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10 humann_reduce_table
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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11 --input '$input'
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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12 -o '$output'
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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13 --function '$function'
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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14 --sort-by '$sort_by'
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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15 ]]></command>
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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16 <inputs>
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17 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway/taxonomic table"/>
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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18 <param argument="--function" type="select" label="Function to apply to select value to keep">
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19 <option value="max" selected="true">Max</option>
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20 <option value="sum">Sum</option>
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21 <option value="mean">Mean</option>
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22 <option value="min">Min</option>
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23 </param>
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24 <param argument="--sort-by" type="select" label="How to sort the output">
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25 <option value="name" selected="true">Name</option>
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26 <option value="value">Value</option>
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27 <option value="level">Level</option>
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28 </param>
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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29 </inputs>
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30 <outputs>
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31 <data format="tabular" name="output"/>
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32 </outputs>
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33 <tests>
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34 <test expect_num_outputs="1">
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35 <param name="input" value="demo_joined_pathabundance_pathcoverage.tsv"/>
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36 <param name="function" value="max"/>
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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37 <param name="sort_by" value="name"/>
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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38 <output name="output" ftype="tabular">
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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39 <assert_contents>
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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40 <has_text text="max" />
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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41 <has_text text="UNINTEGRATED|unclassified" />
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42 <has_text text="PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified" />
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43 </assert_contents>
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44 </output>
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 @HELP_HEADER@
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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49
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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50 This tool reduces a joined HUMAnN table. It selects for each row which value to keep given a function (max, sum, mean or min).
c2488dbc8e39 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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51 ]]></help>
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52 <expand macro="citations"/>
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53 </tool>