view humann_split_table.xml @ 5:e9d12c223a80 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit ccaedf215676efa9afe412f2f8c95d8220c885ee

<tool id="humann_split_table" name="Split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description> a merged HUMAnN table</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_table
    --input '$input'
    -o 'output'
#if $taxonomy_index
    --taxonomy_index '$taxonomy_index'
#end if
#if $taxonomy_level
    --taxonomy_level '$taxonomy_level'
#end if
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular,biom1" label="Gene table to split"/>
        <param argument="--taxonomy_index" type="text" label="Index of the gene in the taxonomy data" optional="true"/>
        <param argument="--taxonomy_level" type="select" label="Level of taxonomy for the output" optional="true" help="If input is from picrust metagenome_contributions.py">
            <option value="Kingdom">Kingdom</option>
            <option value="Phylum">Phylum</option>
            <option value="Class">Class</option>
            <option value="Order">Order</option>
            <option value="Family">Family</option>
            <option value="Genus">Genus</option>
            <option value="Species">Species</option>
        </param>
    </inputs>
    <outputs>
        <collection type="list" name="split_tables">
            <discover_datasets pattern="__designation_and_ext__" directory="output"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="demo_joined_pathabundance_pathcoverage.tsv"/>
            <output_collection name="split_tables" type="list">
                <element name="humann_Abundance" ftype="tsv">
                    <assert_contents>
                        <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
                        <has_n_columns n="2"/>
                    </assert_contents>
                </element>
                <element name="humann_Coverage" ftype="tsv">
                    <assert_contents>
                        <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
                        <has_n_columns n="2"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

This tool splits a merged feature table (multiple samples) into one file per sample. Some analyses can only accept one sample at a time.
    ]]></help>
    <expand macro="citations"/>
</tool>