Mercurial > repos > iuc > humann_split_table

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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 10:00:22 +0000
parents 44cacbe09bfc
children
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506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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1 <tool id="humann_split_table" name="Split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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2 <description> a merged HUMAnN table</description>
506d4a349aa1 "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>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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5 </macros>
506d4a349aa1 "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"/>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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8 <expand macro="version"/>
506d4a349aa1 "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[
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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10 humann_split_table
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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11 --input '$input'
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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12 -o 'output'
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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13 #if $taxonomy_index
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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14 --taxonomy_index '$taxonomy_index'
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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15 #end if
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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16 #if $taxonomy_level
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17 --taxonomy_level '$taxonomy_level'
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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18 #end if
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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19 ]]></command>
506d4a349aa1 "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 argument="--input" type="data" format="tsv,tabular,biom1" label="Gene table to split"/>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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22 <param argument="--taxonomy_index" type="text" label="Index of the gene in the taxonomy data" optional="true"/>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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23 <param argument="--taxonomy_level" type="select" label="Level of taxonomy for the output" optional="true" help="If input is from picrust metagenome_contributions.py">
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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24 <option value="Kingdom">Kingdom</option>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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25 <option value="Phylum">Phylum</option>
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26 <option value="Class">Class</option>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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27 <option value="Order">Order</option>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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28 <option value="Family">Family</option>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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29 <option value="Genus">Genus</option>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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30 <option value="Species">Species</option>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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31 </param>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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32 </inputs>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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33 <outputs>
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34 <collection type="list" name="split_tables">
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35 <discover_datasets pattern="__designation_and_ext__" directory="output"/>
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36 </collection>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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37 </outputs>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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38 <tests>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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39 <test>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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40 <param name="input" value="demo_joined_pathabundance_pathcoverage.tsv"/>
2
44cacbe09bfc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
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41 <output_collection name="split_tables" type="list">
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42 <element name="humann_Abundance" ftype="tsv">
0
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43 <assert_contents>
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44 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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45 <has_n_columns n="2"/>
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46 </assert_contents>
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47 </element>
2
44cacbe09bfc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
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48 <element name="humann_Coverage" ftype="tsv">
0
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49 <assert_contents>
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50 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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51 <has_n_columns n="2"/>
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52 </assert_contents>
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53 </element>
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54 </output_collection>
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55 </test>
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56 </tests>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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57 <help><![CDATA[
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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58 @HELP_HEADER@
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59
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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60 This tool splits a merged feature table (multiple samples) into one file per sample. Some analyses can only accept one sample at a time.
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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61 ]]></help>
506d4a349aa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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62 <expand macro="citations"/>
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63 </tool>