Mercurial > repos > thanhlv > humann_split_table

comparison humann_split_table.xml @ 0:40a24d7612b8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f
author thanhlv
date Mon, 13 Feb 2023 16:17:26 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:40a24d7612b8
1 <tool id="humann_split_table" name="Split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
2 <description> a merged 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_split_table
11 --input '$input'
12 -o 'output'
13 #if $taxonomy_index
14 --taxonomy_index '$taxonomy_index'
15 #end if
16 #if $taxonomy_level
17 --taxonomy_level '$taxonomy_level'
18 #end if
19 ]]></command>
20 <inputs>
21 <param argument="--input" type="data" format="tsv,tabular,biom1" label="Gene table to split"/>
22 <param argument="--taxonomy_index" type="text" label="Index of the gene in the taxonomy data" optional="true"/>
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">
24 <option value="Kingdom">Kingdom</option>
25 <option value="Phylum">Phylum</option>
26 <option value="Class">Class</option>
27 <option value="Order">Order</option>
28 <option value="Family">Family</option>
29 <option value="Genus">Genus</option>
30 <option value="Species">Species</option>
31 </param>
32 </inputs>
33 <outputs>
34 <collection type="list" name="split_tables">
35 <discover_datasets pattern="__designation_and_ext__" directory="output"/>
36 </collection>
37 </outputs>
38 <tests>
39 <test>
40 <param name="input" value="demo_joined_pathabundance_pathcoverage.tsv"/>
41 <output_collection name="split_tables" type="list">
42 <element name="humann_Abundance" ftype="tsv">
43 <assert_contents>
44 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
45 <has_n_columns n="2"/>
46 </assert_contents>
47 </element>
48 <element name="humann_Coverage" ftype="tsv">
49 <assert_contents>
50 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
51 <has_n_columns n="2"/>
52 </assert_contents>
53 </element>
54 </output_collection>
55 </test>
56 </tests>
57 <help><![CDATA[
58 @HELP_HEADER@
59
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.
61 ]]></help>
62 <expand macro="citations"/>
63 </tool>