<tool id="humann_join_tables" name="Join (merge)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single table</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
#import re
mkdir tmp_dir
&&
#for $input in $inputs
ln -s '$input' 'tmp_dir/${re.sub('[^\w\-_.]', '_', input.element_identifier)}' &&
#end for
humann_join_tables
    -i 'tmp_dir'
    -o '$output'
    ]]></command>
    <inputs>
        <param name="inputs" type="data" format="tsv,tabular" multiple="true" label="Gene/pathway table"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="inputs" value="demo_pathabundance.tsv,demo_pathcoverage.tsv"/>
            <output name="output" ftype="tabular" value="demo_joined_pathabundance_pathcoverage.tsv">
                <assert_contents>
                    <has_text text="humann_Abundance" />
                    <has_text text="humann_Coverage" />
                    <has_text text="UNINTEGRATED|unclassified" />
                    <has_text text="PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

This tool joins (merges) multiple single-sample output files into a single table with multiple samples.
It can also be used to join multiple multi-sample output files into a single table.
    ]]></help>
    <expand macro="citations"/>
</tool>