view humann_split_stratified_table.xml @ 0:75bedfb2078b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"

<tool id="humann_split_stratified_table" name="Split a HUMAnN table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>into 2 tables (one stratified and one unstratified)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann_split_stratified_table
    --input '$input'
    --output 'output'
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular" label="Stratified input table"/>
    </inputs>
    <outputs>
        <data format="tabular" name="stratified" from_work_dir="output/*_stratified*" label="${tool.name} on ${on_string}: Stratified table"/>
        <data format="tabular" name="unstratified" from_work_dir="output/*_unstratified*" label="${tool.name} on ${on_string}: Unstratified table"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="input" value="demo_genefamilies.tsv"/>
            <output name="stratified" ftype="tabular">
                <assert_contents>
                    <has_text text="UniRef90_A0A174QBF2|g__Bacteroides.s__Bacteroides_vulgatus" />
                    <has_text text="UniRef90_A0A3E5DKA1|g__Bacteroides.s__Bacteroides_vulgatus" />
                </assert_contents>
            </output>
            <output name="unstratified" ftype="tabular">
                <assert_contents>
                    <has_text text="UniRef90_A0A174QBF2" />
                    <not_has_text text="UniRef90_A0A174QBF2|g__Bacteroides.s__Bacteroides_vulgatus" />
                    <has_text text="UniRef90_A0A3E5DKA1" />
                    <not_has_text text="UniRef90_A0A3E5DKA1|g__Bacteroides.s__Bacteroides_vulgatus" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

This tool splits a stratified table into two files (one stratified and one unstratified).
    ]]></help>
    <expand macro="citations"/>
</tool>