annotate humann_rename_table.xml @ 0:d24841f5c3d2 draft

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

<tool id="humann_rename_table" name="Rename features" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>of a HUMAnN generated 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_rename_table
    --input '$input'
    -o '$output'
#if $renaming.type == 'standard'
    --names '$renaming.names'
#else if $renaming.type == 'advanced'
    --custom '$renaming.names.fields.path'
#else
    --custom '$renaming.custom'
#end if
    $simplify 
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
        <conditional name="renaming">
            <param name="type" type="select" label="Type of feature renaming">
                <option value="standard">Basic feature renaming</option>
                <option value="advanced">Advanced feature renaming</option>
                <option value="custom">Custom feature renaming</option>
            </param>
            <when value="standard">
                <param argument="--names" type="select" label="Features to be renamed" help="More features can be renamed with advanced mode">
                    <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
                    <option value="metacyc-pwy">MetaCyc pathways</option>
                    <option value="infogo1000">InfoGO1000</option>
                    <option value="kegg-module">KEGG Module</option>
                    <option value="ec">Enzyme commision (EC)</option>
                    <option value="go">Gene Ontology (GO)</option>
                    <option value="pfam">PFAM</option>
                    <option value="eggnog">eggNOG</option>
                    <option value="kegg-pathway">KEGG Pathway</option>
                    <option value="kegg-orthology">KEGG Orthology</option>
                </param>
            </when>
            <when value="advanced">
                <param name="names" type="select" label="Features to be renamed">
                    <options from_data_table="humann_utility_mapping">
                        <validator message="No utility mapping is available" type="no_options" />
                        <filter type="regexp" column="0" value=".*name" keep="true" />
                    </options>
                </param>
            </when>
            <when value="custom">
                <param argument="--custom" type="data" format="tsv,tabular" label="Mapping file" help="The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new value"/>
            </when>
        </conditional>
        <param argument="--simplify" type="boolean" truevalue="--simplify" falsevalue="" checked="false" label="Remove non-alphanumeric characters from names?"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/>
            <conditional name="renaming">
                <param name="type" value="standard"/>
                <param name="names" value="infogo1000" />
            </conditional>
            <param name="simplify" value=""/>
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_text text="GO:0000015: [CC] phosphopyruvate hydratase complex" />
                    <has_text text="GO:0000287: [MF] magnesium ion binding" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input" value="demo_genefamilies.tsv"/>
            <conditional name="renaming">
                <param name="type" value="advanced"/>
                <param name="names" value="utility_mapping-full-map_uniref90_name-3.0.0-29042021"/>
            </conditional>
            <param name="simplify" value=""/>
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_text text="UniRef90_A6L2T0: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" />
                    <has_text text="UniRef90_U5FT06: Hexosyltransferase|unclassified" />
                    <has_text text="UniRef90_Q8GT21: Benzyl alcohol O-benzoyltransferase|unclassified" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input" value="demo_genefamilies.tsv"/>
            <conditional name="renaming">
                <param name="type" value="custom"/>
                <param name="custom" value="test-db/utility_mapping/map_uniref90_name.txt" />
            </conditional>
            <param name="simplify" value=""/>
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_text text="UniRef90_A6L2T0: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" />
                    <has_text text="UniRef90_U5FT06: Hexosyltransferase|unclassified" />
                    <has_text text="UniRef90_Q8GT21: Benzyl alcohol O-benzoyltransferase|unclassified" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

By default, HUMAnN outputs do not attach names (glosses) to individual feature IDs to keep file sizes down. 
This tool is used to attach those names.

The most common use for this tool is attaching gene names to UniRef90/UniRef50 features in the default gene family output files.
Features without names (common for many UniRef90/50 families) are assigned the default name: NO_NAME.
    ]]></help>
    <expand macro="citations"/>
</tool>