annotate get_term_id_vs_term_name.xml @ 0:b2471db454a0 draft default tip

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_name" name="Get all the term IDs and term names" 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_name.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 name" />
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="pre_cco_core.obo"/>
            <output name="output" file="term_id_vs_term_name.tab"/>
        </test>
    </tests>
    <help>

.. class:: infomark

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


**Example**

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

  GO:0050129	N-formylglutamate deformylase activity
  GO:0051663	oocyte nucleus localization involved in oocyte dorsal/ventral axis specification
  GO:0051712	positive regulation of killing of cells of another organism
  GO:0033972	proclavaminate amidinohydrolase activity
  GO:0032513	negative regulation of protein phosphatase type 2B activity
  GO:0008711	ADP-L-glycero-D-manno-heptose synthase activity
  GO:0006285	base-excision repair, AP site formation
  GO:0043527	tRNA methyltransferase complex
  ...
  ...

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