Mercurial > repos > iuc > humann_unpack_pathways

comparison humann_genefamilies_genus_level @ 0:c3d043160f09 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 09:07:12 +0000
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-1:000000000000 0:c3d043160f09
1 <!-- The tool is broken with current version of HUMAnN. Once it will be fixed (PR merged), we can update this wrapper and add the XML extension to enable it -->
2 <tool id="humann_genefamilies_genus_level" name="Create a genus level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>gene families and pathways from HUMAnN species level gene families</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="edam_ontology"/>
8 <expand macro="requirements"/>
9 <expand macro="version"/>
10 <command detect_errors="exit_code"><![CDATA[
11 humann_genefamilies_genus_level
12 --input '$input'
13 --output '$gene_families'
14 &&
15 humann
16 --input '$gene_families'
17 --output '$pathways'
18 ]]></command>
19 <inputs>
20 <param argument="--input" type="data" format="tsv,tabular" label="Species level gene families" help="Direct output from HUMAnN"/>
21 </inputs>
22 <outputs>
23 <data name="gene_families" format="tabular" label="${tool.name} on ${on_string}: Genus level gene families"/>
24 <data name="pathways" format="tabular" label="${tool.name} on ${on_string}: Genus level pathways"/>
25 </outputs>
26 <tests>
27 <test expect_num_outputs="1">
28 <param name="input" value="demo_genefamilies.tsv"/>
29 <output name="gene_families" ftype="tabular" value="genus-level-gene-families.tsv" compare="sim_size">
30 <assert_contents>
31 <has_text text="humann_Abundance"/>
32 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
33 <has_n_columns n="2"/>
34 </assert_contents>
35 </output>
36 <output name="pathways" ftype="tabular" value="genus-level-pathways.tsv" compare="sim_size">
37 <assert_contents>
38 <has_text text="humann_Abundance"/>
39 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
40 <has_n_columns n="2"/>
41 </assert_contents>
42 </output>
43 </test>
44 </tests>
45 <help><![CDATA[
46 @HELP_HEADER@
47
48 By default, the gene families and pathways output files from HUMAnN are species level.
49 This tool generates genus level gene families and pathways
50 ]]></help>
51 <expand macro="citations"/>
52 </tool>