annotate get_ancestor_terms.xml @ 0:ac306663d53f draft

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

<tool id="onto_tk_get_ancestor_terms" name="Get the ancestor terms of a given OBO term" version="@VERSION@.0">
    <description>Collects the ancestor terms from a given term in the given OBO ontology</description>
    <macros>
        <import>onto_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
        get_ancestor_terms.pl
            -f '$input'
            -t '$term_id' > '$output'
    </command>
    <inputs>
        <param format="text" name="input" type="data" label="Source file"/>
        <expand macro="term_id" />
    </inputs>
    <outputs>
        <data format="tabular" name="output">
            <actions>
                <action name="column_names" type="metadata" default="term ID,term name" />
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="pre_cco_core.obo" ftype="obo"/>
            <param name="term_id" value="CCO:P0000020"/>
            <output name="output" file="ancestors.tab"/>
        </test>
    </tests>
    <help>

.. class:: infomark

Collects the ancestor terms (list of IDs) from a given term (existing ID) in the given OBO ontology.

**Example**

If you ask for the descendents of the Gene Ontology term with ID **GO:000800** you will get::

  GO:0043229	intracellular organelle
  GO:0043232	intracellular non-membrane-bounded organelle
  GO:0044446	intracellular organelle part
  GO:0044424	intracellular part
  GO:0005623	cell
  GO:0044422	organelle part
  GO:0043228	non-membrane-bounded organelle
  GO:0044427	chromosomal part
  GO:0005575	cellular_component
  GO:0000793	condensed chromosome
  GO:0043231	intracellular membrane-bounded organelle
  GO:0043226	organelle
  GO:0005634	nucleus
  GO:0044464	cell part
  GO:0005622	intracellular
  GO:0044454	nuclear chromosome part
  GO:0005694	chromosome
  GO:0000228	nuclear chromosome
  GO:0043227	membrane-bounded organelle
  GO:0000794	condensed nuclear chromosome
  GO:0000795	synaptonemal complex
  GO:0044428	nuclear part

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