annotate cat_add_names.xml @ 3:21bf2f07f3f3 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 47be73f0ca2b3a3bcb79a1fa7cf15a63c7facd19

<tool id="cat_add_names" name="CAT add_names" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>annotate with taxonomic names</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <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 from CAT contigs or CAT bins"/>
        <expand macro="cat_db" />
        <expand macro="add_names_options" />
    </inputs>
    <outputs>
        <data name="output" format="tabular"  label="#set name = $input.name.replace('.txt','.names.txt')# $name"/>
    </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.  Names can be added to ORF2LCA.txt, contig2classification.txt, and bin2classification.txt outputs. 

@COMMON_HELP@

**INPUT**

Example: contig2classification.txt from CAT conitgs

::

  # contig        classification  reason  lineage lineage scores
  contig_44250    classified      based on 1/2 ORFs       1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00
  contig_9952     classified      based on 1/5 ORFs       1;131567;2;1783272;1239;91061*  1.00;1.00;1.00;1.00;1.00;1.00


**OUTPUT**

::

  # contig        classification  reason  lineage lineage scores  superkingdom    phylum  class   order   family  genus   species
  contig_44250    classified      based on 1/2 ORFs       1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00    Bacteria: 1.00  Proteobacteria: 1.00    Gammaproteobacteria: 1.00       Vibrionales: 1.00       Vibrionaceae: 1.00      Vibrio: 1.00    Vibrio cholerae: 1.00
  contig_9952     classified      based on 1/5 ORFs       1;131567;2;1783272;1239;91061*  1.00;1.00;1.00;1.00;1.00;1.00   Bacteria: 1.00  Firmicutes: 1.00        Bacilli*: 1.00  not classified  not classified  not classified  not classified


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.

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