annotate add_descriptions.xml @ 1:2f47a294ef49 draft default tip

planemo upload for repository https://github.com/picrust/picrust2 commit f8c32a316582ff102c9b7edf3817000691ef9eea

<tool id="picrust2_add_descriptions" name="PICRUSt2 Add descriptions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>column to a function abundance table</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tool"/>
    <expand macro="requirements"/>
    <version_command>add_descriptions.py -v</version_command>
    <command detect_errors="exit_code"><![CDATA[
add_descriptions.py
    --input '$input'
    --output '$func_abun_table_description'
#if $map_file.selector == "default"
    --map_type '$map_file.map_type'
#else if $map_file.selector == "custom"
    --custom_map_table '$map_file.custom_map_table'
#end if
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tabular" label="Input function (gene family or pathway) abundance table"/>
        <conditional name="map_file">
            <param name="selector" type="select" label="Argument specifying non-default reference files to use for sequence placement">
                <option value="default" selected="true">Default mapping file</option>
                <option value="custom">Customized mapping file</option>
            </param>
            <when value="default">
                <param argument="--map_type" type="select" label="Mapping table to use">
                    <option value="COG">Clusters of Orthologous Genes database (COG)</option>
                    <option value="EC">Enzyme Commission number database (EC number)</option>
                    <option value="KO">KEGG Orthology database (KO)</option>
                    <option value="PFAM">Pfam database</option>
                    <option value="TIGRFAM">TIGRFAM database</option>
                    <option value="METACYC">Metabolic Pathway database (MetaCyc)</option>
                </param>
            </when>
            <when value="custom">
                <param argument="--custom_map_table" type="data" format="tabular" label="Custom mapping table" help="A table with at least two columns linking function ids to descriptions for each function">
                    <validator type="dataset_metadata_in_range" metadata_name="columns" min="2" message="Input needs to have at least two columns"/>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="func_abun_table_description" format="tabular" from_work_dir="added_description.tsv"/>
    </outputs>
    <tests>
    <test expect_num_outputs="1">
        <param name="input" value="pred_metagenome_unstrat.tsv.gz"/>
        <conditional name="map_file">
            <param name="selector" value="default"/>
            <param name="map_type" value="EC"/>
        </conditional>
        <output name="func_abun_table_description">
            <assert_contents>
                <has_text text="description"/>
                <has_n_lines n="1000"/>
            </assert_contents>
        </output>
    </test>
    <test expect_num_outputs="1">
        <param name="input" value="pred_metagenome_unstrat.tsv.gz"/>
        <conditional name="map_file">
            <param name="selector" value="custom"/>
            <param name="custom_map_table" value="ec_unstrat_test.txt.gz"/>
        </conditional>
        <output name="func_abun_table_description">
            <assert_contents>
                <has_text text="description"/>
                <has_n_lines n="1000"/>
            </assert_contents>
        </output>
    </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Add Descriptions
================
Adds a description column to a function abundance table and outputs a new file.

Note
====
The user needs to specify the input file and what type of functions are in the input table. Will throw an error if no ids overlap and otherwise will fill in "not_found" for the description of ids in the function table not in the mapfile.

Input
=====
Input function abundance table.

Output
======
Output function abundance table with added description column.
    ]]></help>
    <citations>
        <citation type="doi">10.1038/s41587-020-0548-6</citation>
    </citations>
</tool>