diff funDo.xml @ 0:64133669255f draft

Uploaded tool tarball.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/funDo.xml	Wed Sep 25 11:22:47 2013 -0400
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+<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_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>