annotate cat_add_names.xml @ 5:226949352e31 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit a1c079107b72dc08612fa664897bb9d627624e52-dirty

<tool id="cat_add_names" name="CAT add_names" version="@VERSION@.0">
    <description>annotate with taxonomic classification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
    CAT add_names -i '$input'
    @CAT_TAXONOMY@
    @ADD_NAMES_OPTIONS@
    -o output_names.txt
    && @TXT2TSV@ -i output_names.txt -o $output
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tabular,txt" label="classification.txt or ORF2LCA.txt"/>
        <expand macro="cat_db" />
        <expand macro="add_names_options" />
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="tabular" value="test_contig.contig2classification.txt"/>
            <expand macro="test_catdb"/>
            <output name="output">
                <assert_contents>
                    <has_text text="Firmicutes" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**CAT/BAT add_names** 

Add taxonomic names to CAT or BAT output files.

Required arguments:
  -i, --input_file       Path to input file. Can be either classification
                         output file or ORF2LCA output file.
  -t, --taxonomy_folder  Path to folder that contains taxonomy files.

Optional arguments:
  --only_official        Only output official level names.
  --exclude_scores       Do not include bit-score support scores in the
                         lineage.

@COMMON_HELP@
    ]]></help>
    <expand macro="citations" />
</tool>