Mercurial > repos > iuc > gemini
comparison gemini_interactions.xml @ 20:b5207530f991 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
| author | iuc |
|---|---|
| date | Tue, 29 Dec 2015 10:19:47 -0500 |
| parents | 27ce3de83007 |
| children |
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| 19:27ce3de83007 | 20:b5207530f991 |
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| 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> | |
| 2 <description>Find genes among variants that are interacting partners</description> | |
| 3 <macros> | |
| 4 <import>gemini_macros.xml</import> | |
| 5 <token name="@BINARY@">interactions</token> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <expand macro="stdio" /> | |
| 9 <expand macro="version_command" /> | |
| 10 <command> | |
| 11 <![CDATA[ | |
| 12 gemini | |
| 13 --annotation-dir ${annotation_databases.fields.path} | |
| 14 #if $gene.gene_selector == 'lof': | |
| 15 ## lof interactions is a separate program | |
| 16 lof_interactions | |
| 17 #else: | |
| 18 ## use normal gemini interactions program | |
| 19 @BINARY@ | |
| 20 -g "${gene.gene}" | |
| 21 #end if | |
| 22 | |
| 23 -r "${radius}" | |
| 24 $variant_mode | |
| 25 "${ infile }" | |
| 26 > "${ outfile }" | |
| 27 ]]> | |
| 28 </command> | |
| 29 <inputs> | |
| 30 <expand macro="infile" /> | |
| 31 | |
| 32 <conditional name="gene"> | |
| 33 <param name="gene_selector" type="select" label="Studying" help=""> | |
| 34 <option value="gene">Interesting gene</option> | |
| 35 <option value="lof">All loss-of-function variants</option> | |
| 36 </param> | |
| 37 <when value="gene"> | |
| 38 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" /> | |
| 39 </when> | |
| 40 <when value="lof"/> | |
| 41 </conditional> | |
| 42 <expand macro="annotation_dir" /> | |
| 43 <expand macro="radius" /> | |
| 44 <expand macro="variant_mode" /> | |
| 45 </inputs> | |
| 46 <outputs> | |
| 47 <data name="outfile" format="tabular" /> | |
| 48 </outputs> | |
| 49 <tests> | |
| 50 <test> | |
| 51 </test> | |
| 52 </tests> | |
| 53 <help> | |
| 54 **What it does** | |
| 55 | |
| 56 Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data. | |
| 57 Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the | |
| 58 protein itself. We have used the HPRD_ binary interaction data to build a p-p network graph which can be explored by GEMINI. | |
| 59 | |
| 60 .. _HPRD: http://www.ncbi.nlm.nih.gov/pubmed/18988627 | |
| 61 | |
| 62 | |
| 63 @CITATION@ | |
| 64 </help> | |
| 65 <expand macro="citations"> | |
| 66 <citation type="doi">10.1093/nar/gkn892</citation><!-- HPRD citation --> | |
| 67 </expand> | |
| 68 </tool> |