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comparison humann_reduce_table.xml @ 0:c2488dbc8e39 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
author iuc
date Wed, 12 May 2021 09:00:46 +0000
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1 <tool id="humann_reduce_table" name="Reduce" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>a joined HUMAnN table</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_ontology"/>
7 <expand macro="requirements"/>
8 <expand macro="version"/>
9 <command detect_errors="exit_code"><![CDATA[
10 humann_reduce_table
11 --input '$input'
12 -o '$output'
13 --function '$function'
14 --sort-by '$sort_by'
15 ]]></command>
16 <inputs>
17 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway/taxonomic table"/>
18 <param argument="--function" type="select" label="Function to apply to select value to keep">
19 <option value="max" selected="true">Max</option>
20 <option value="sum">Sum</option>
21 <option value="mean">Mean</option>
22 <option value="min">Min</option>
23 </param>
24 <param argument="--sort-by" type="select" label="How to sort the output">
25 <option value="name" selected="true">Name</option>
26 <option value="value">Value</option>
27 <option value="level">Level</option>
28 </param>
29 </inputs>
30 <outputs>
31 <data format="tabular" name="output"/>
32 </outputs>
33 <tests>
34 <test expect_num_outputs="1">
35 <param name="input" value="demo_joined_pathabundance_pathcoverage.tsv"/>
36 <param name="function" value="max"/>
37 <param name="sort_by" value="name"/>
38 <output name="output" ftype="tabular">
39 <assert_contents>
40 <has_text text="max" />
41 <has_text text="UNINTEGRATED|unclassified" />
42 <has_text text="PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified" />
43 </assert_contents>
44 </output>
45 </test>
46 </tests>
47 <help><![CDATA[
48 @HELP_HEADER@
49
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).
51 ]]></help>
52 <expand macro="citations"/>
53 </tool>