Mercurial > repos > devteam > hgv_fundo
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
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:50:04 -0500 |
| parents | 64133669255f |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="hgv_funDo" name="FunDO" version="1.0.0"> |
| 2 <description>human genes associated with disease terms</description> | |
| 3 | |
| 4 <command interpreter="perl"> | |
| 5 disease_ontology_gene_fuzzy_selector.pl $build $out_file1 ${GALAXY_DATA_INDEX_DIR}/funDo.loc '$term' | |
| 6 </command> | |
| 7 | |
| 8 <inputs> | |
| 9 <param name="build" type="select" label="Database build"> | |
| 10 <options from_file="funDo.loc"> | |
| 11 <column name="name" index="0"/> | |
| 12 <column name="value" index="0"/> | |
| 13 <filter type="unique_value" column="0"/> | |
| 14 </options> | |
| 15 </param> | |
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ca3fcd18dc3e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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16 <param name="term" type="text" label="Disease term(s)" /> |
| 0 | 17 </inputs> |
| 18 | |
| 19 <outputs> | |
| 20 <data format="interval" name="out_file1"> | |
| 21 </data> | |
| 22 </outputs> | |
| 23 | |
| 24 <tests> | |
| 25 <test> | |
| 26 <param name="term" value="lung"/> | |
| 27 <param name="build" value="hg18"/> | |
| 28 <output name="out_file1" file="funDo_output1.interval" /> | |
| 29 </test> | |
| 30 </tests> | |
| 31 | |
| 32 <help> | |
| 33 **Dataset formats** | |
| 34 | |
| 35 There is no input dataset. The output is in interval_ format. | |
| 36 | |
| 37 .. _interval: ${static_path}/formatHelp.html#interval | |
| 38 | |
| 39 ----- | |
| 40 | |
| 41 **What it does** | |
| 42 | |
| 43 This tool searches the disease-term field of the DOLite mappings | |
| 44 used by the FunDO project and returns a set of genes that | |
| 45 are associated with terms matching the specified pattern. (This is the | |
| 46 reverse of what FunDO's own server does.) | |
| 47 | |
| 48 The search is case insensitive, and selects terms that contain any of | |
| 49 the given words, either exactly or within a longer word (e.g. "nemia" | |
| 50 selects not only "anemia", but also "hyperglycinemia", "tyrosinemias", | |
| 51 and many other things). Multiple words should be separated by spaces, | |
| 52 not commas. As a special case, entering the word "disease" returns all | |
| 53 genes associated with any disease, even if that word does not actually | |
| 54 appear in the term field. | |
| 55 | |
| 56 Website: http://django.nubic.northwestern.edu/fundo/ | |
| 57 | |
| 58 ----- | |
| 59 | |
| 60 **Example** | |
| 61 | |
| 62 Typing:: | |
| 63 | |
| 64 carcinoma | |
| 65 | |
| 66 results in:: | |
| 67 | |
| 68 1. 2. 3. 4. 5. 6. 7. | |
| 69 chr11 89507465 89565427 + NAALAD2 10003 Adenocarcinoma | |
| 70 chr15 50189113 50192264 - BCL2L10 10017 Carcinoma | |
| 71 chr7 150535855 150555250 - ABCF2 10061 Clear cell carcinoma | |
| 72 chr7 150540508 150555250 - ABCF2 10061 Clear cell carcinoma | |
| 73 chr10 134925911 134940397 - ADAM8 101 Adenocarcinoma | |
| 74 chr10 134925911 134940397 - ADAM8 101 Adenocarcinoma | |
| 75 etc. | |
| 76 | |
| 77 where the column contents are as follows:: | |
| 78 | |
| 79 1. chromosome name | |
| 80 2. start position of the gene | |
| 81 3. end position of the gene | |
| 82 4. strand | |
| 83 4. gene name | |
| 84 6. Entrez Gene ID | |
| 85 7. disease term | |
| 86 | |
| 87 ----- | |
| 88 | |
| 89 **References** | |
| 90 | |
| 91 Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM. (2009) | |
| 92 From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose | |
| 93 ontology for the test of gene-ontology associations. | |
| 94 Bioinformatics. 25(12):i63-8. | |
| 95 | |
| 96 Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL. (2009) | |
| 97 Annotating the human genome with Disease Ontology. | |
| 98 BMC Genomics. 10 Suppl 1:S6. | |
| 99 | |
| 100 </help> | |
| 101 </tool> |