Mercurial > repos > iuc > humann2_split_table

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 8d953926efdf23d8c3fb8719341dff51a55a92f2"
author iuc
date Sun, 28 Mar 2021 06:51:46 +0000
parents 9aef81ff786b
children
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9aef81ff786b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
iuc
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1 <tool id="humann2_split_table" name="Split" version="@WRAPPER_VERSION@.1">
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2 <description> a HUMAnN2 generated table</description>
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3 <macros>
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4 <import>humann2_macros.xml</import>
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5 </macros>
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9aef81ff786b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
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6 <expand macro="stdio"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 humann2_split_table
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11 --input '$input'
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12 -o 'output'
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13 #if $taxonomy_index
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14 --taxonomy_index '$taxonomy_index'
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15 #end if
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16 #if $taxonomy_level
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17 --taxonomy_level '$taxonomy_level'
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18 #end if
0
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19 ]]></command>
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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"/>
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22 <param argument="--taxonomy_index" type="text" label="Index of the gene in the taxonomy data" optional="true"/>
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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">
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24 <option value="Kingdom">Kingdom</option>
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25 <option value="Phylum">Phylum</option>
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26 <option value="Class">Class</option>
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27 <option value="Order">Order</option>
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28 <option value="Family">Family</option>
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29 <option value="Genus">Genus</option>
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30 <option value="Species">Species</option>
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <collection type="list" name="split_tables" label="${tool.name} on ${on_string}: Split tables">
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35 <discover_datasets pattern="__designation_and_ext__" directory="output"/>
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36 </collection>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="input" value="joined_pathway_coverage_abundance.tsv"/>
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41 <output_collection name="split_tables" type="list" >
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42 <element name="demo_Coverage" file="demo_Coverage.tsv" />
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43 <element name="demo_Abundance" file="demo_Abundance.tsv" />
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44 </output_collection>
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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@
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49
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50 Split HUMAnN2 table is a tool to split a gene table with multiple columns. This file can have been generated with the join table tool.
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51 ]]></help>
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52 <expand macro="citations"/>
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53 </tool>