Mercurial > repos > iuc > humann_join_tables

comparison humann_join_tables.xml @ 0:cf7f80d59099 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 09:02:06 +0000
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1 <tool id="humann_join_tables" name="Join (merge)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single 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 #import re
11 mkdir tmp_dir
12 &&
13 #for $input in $inputs
14 ln -s '$input' 'tmp_dir/${re.sub('[^\w\-_.]', '_', input.element_identifier)}' &&
15 #end for
16 humann_join_tables
17 -i 'tmp_dir'
18 -o '$output'
19 ]]></command>
20 <inputs>
21 <param name="inputs" type="data" format="tsv,tabular" multiple="true" label="Gene/pathway table"/>
22 </inputs>
23 <outputs>
24 <data format="tabular" name="output"/>
25 </outputs>
26 <tests>
27 <test expect_num_outputs="1">
28 <param name="inputs" value="demo_pathabundance.tsv,demo_pathcoverage.tsv"/>
29 <output name="output" ftype="tabular" value="demo_joined_pathabundance_pathcoverage.tsv">
30 <assert_contents>
31 <has_text text="humann_Abundance" />
32 <has_text text="humann_Coverage" />
33 <has_text text="UNINTEGRATED|unclassified" />
34 <has_text text="PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified" />
35 </assert_contents>
36 </output>
37 </test>
38 </tests>
39 <help><![CDATA[
40 @HELP_HEADER@
41
42 This tool joins (merges) multiple single-sample output files into a single table with multiple samples.
43 It can also be used to join multiple multi-sample output files into a single table.
44 ]]></help>
45 <expand macro="citations"/>
46 </tool>