comparison 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

4:aaeb63501369

    @ADD_NAMES_OPTIONS@
    -o output_names.txt
    && @TXT2TSV@ -i output_names.txt -o $output
    ]]></command>
    <inputs>
        <param name="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"/>

            </output>
        </test>
    </tests>
    <help><![CDATA[
**CAT/BAT add_names** 
Add names for the NCBI taxomy IDs.

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

5:226949352e31

    @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"/>

            </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>