annotate funDo.xml @ 1:ca3fcd18dc3e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo commit a1517c9d22029095120643bbe2c8fa53754dd2b7

<tool id="hgv_funDo" name="FunDO" version="1.0.0">
  <description>human genes associated with disease terms</description>

  <command interpreter="perl">
    disease_ontology_gene_fuzzy_selector.pl $build $out_file1 ${GALAXY_DATA_INDEX_DIR}/funDo.loc '$term'
  </command>

  <inputs>
    <param name="build" type="select" label="Database build">
      <options from_file="funDo.loc">
        <column name="name" index="0"/>
        <column name="value" index="0"/>
        <filter type="unique_value" column="0"/>
      </options>
    </param>
    <param name="term" type="text" label="Disease term(s)" />
  </inputs>

  <outputs>
    <data format="interval" name="out_file1">
    </data>
  </outputs>

  <tests>
    <test>
      <param name="term" value="lung"/>
      <param name="build" value="hg18"/>
      <output name="out_file1" file="funDo_output1.interval" />
    </test>
  </tests>

  <help>
**Dataset formats**

There is no input dataset.  The output is in interval_ format.

.. _interval: ${static_path}/formatHelp.html#interval

-----

**What it does**

This tool searches the disease-term field of the DOLite mappings
used by the FunDO project and returns a set of genes that 
are associated with terms matching the specified pattern.  (This is the
reverse of what FunDO's own server does.)

The search is case insensitive, and selects terms that contain any of
the given words, either exactly or within a longer word (e.g. "nemia"
selects not only "anemia", but also "hyperglycinemia", "tyrosinemias",
and many other things).  Multiple words should be separated by spaces,
not commas.  As a special case, entering the word "disease" returns all
genes associated with any disease, even if that word does not actually
appear in the term field.

Website: http://django.nubic.northwestern.edu/fundo/

-----

**Example**

Typing:: 

    carcinoma

results in::

    1.     2.         3.         4. 5.       6.     7.
    chr11  89507465   89565427   +  NAALAD2  10003  Adenocarcinoma
    chr15  50189113   50192264   -  BCL2L10  10017  Carcinoma
    chr7   150535855  150555250  -  ABCF2    10061  Clear cell carcinoma
    chr7   150540508  150555250  -  ABCF2    10061  Clear cell carcinoma
    chr10  134925911  134940397  -  ADAM8    101    Adenocarcinoma
    chr10  134925911  134940397  -  ADAM8    101    Adenocarcinoma
    etc.

where the column contents are as follows::

 1. chromosome name
 2. start position of the gene
 3. end position of the gene
 4. strand
 4. gene name
 6. Entrez Gene ID
 7. disease term

-----

**References**

Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM. (2009)
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose
ontology for the test of gene-ontology associations.
Bioinformatics. 25(12):i63-8.

Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL. (2009)
Annotating the human genome with Disease Ontology.
BMC Genomics. 10 Suppl 1:S6.

  </help>
</tool>