/tools/human_genome_variation/funDo.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 101 lines · 76 code · 25 blank · 0 comment · 0 complexity · 35be3a9b20bbbcbbb3b1059d39e4dc71 MD5 · raw file
- <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" size="40" 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/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>