annotate get_term_id_vs_term_def.xml @ 0:4d1fb16ff86a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 9422f839ae354d4c26b02d4494abdeaad518d0e6

<tool id="onto_tk_term_id_vs_term_def" name="Get all the term IDs and term definitions" version="@VERSION@.0">
    <description>of a given OBO ontology</description>
    <macros>
        <import>onto_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
        get_term_id_vs_term_def.pl
        -f '$input' > '$output'
    </command>
    <inputs>
        <expand macro="input_ontology" />
    </inputs>
    <outputs>
        <data format="tabular" name="output">
            <actions>
                <action name="column_names" type="metadata" default="term ID,term definition" />
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="pre_cco_core.obo"/>
            <output name="output" file="term_id_vs_term_def.tab"/>
        </test>
    </tests>
    <help>

.. class:: infomark

Generates a flat file with two columns (TAB separated) with the term_id and term_definition from the elements of the given OBO ontology.


**Example**

If you ask for the term IDs and terms definitions of the Gene Ontology, you will get::

  GO:0006285	The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.
  GO:0043527	A multimeric protein complex involved in the methylation of specific nucleotides in tRNA.
  GO:0005593	Any collagen polymer associated with collagen fibrils and in which the collagen monomers contain two or more relatively short triple-helical domains connected by non-triple-helical sequences; the acronym FACIT stands for fibril-associated collagen with interrupted triple helix.
  GO:0015777	The directed movement of teichoic acid into, out of, within or between cells by means of some external agent such as a transporter or pore. Teichoic acid is any polymer occurring in the cell wall, membrane or capsule of Gram-positive bacteria and containing chains of glycerol phosphate or ribitol phosphate residues.
  GO:0047104	Catalysis of the reaction: NAD+ + CoA + palmitaldehyde = NADH + palmityl-CoA.
  GO:0018302	The incorporation of iron into a 4Fe-4S iron-sulfur cluster via tris-L-cysteinyl-L-N1'-histidino tetrairon tetrasulfide.
  ...
  ...

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