Mercurial > repos > iuc > gemini
comparison gemini_interactions.xml @ 0:14caa57eca63 draft
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| author | iuc |
|---|---|
| date | Mon, 11 Aug 2014 07:44:30 -0400 |
| parents | |
| children | e6512af21622 |
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| -1:000000000000 | 0:14caa57eca63 |
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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 <expand macro="requirements" /> | |
| 4 <expand macro="version_command" /> | |
| 5 <macros> | |
| 6 <import>gemini_macros.xml</import> | |
| 7 <token name="@BINARY@">interactions</token> | |
| 8 </macros> | |
| 9 <command> | |
| 10 <![CDATA[ | |
| 11 gemini | |
| 12 #if $gene.gene_selector == 'lof': | |
| 13 ## lof interactions is a separate program | |
| 14 lof_interactions | |
| 15 #else: | |
| 16 ## use normal gemini interactions program | |
| 17 @BINARY@ | |
| 18 -g "${gene.gene}" | |
| 19 #end if | |
| 20 | |
| 21 -r "${radius}" | |
| 22 $var | |
| 23 "${ infile }" | |
| 24 > "${ outfile }" | |
| 25 ]]> | |
| 26 | |
| 27 loss-of-function | |
| 28 | |
| 29 </command> | |
| 30 <expand macro="stdio" /> | |
| 31 <inputs> | |
| 32 <param name="infile" type="data" format="sqlite" label="GEMINI database" /> | |
| 33 | |
| 34 <conditional name="gene"> | |
| 35 <param name="gene_selector" type="select" label="Studying ..." help=""> | |
| 36 <option value="gene">Interesting gene</option> | |
| 37 <option value="lof">All loss-of-function variants</option> | |
| 38 </param> | |
| 39 <when value="gene"> | |
| 40 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" /> | |
| 41 </when> | |
| 42 <when value="lof"/> | |
| 43 </conditional> | |
| 44 <expand macro="radius" /> | |
| 45 <expand macro="variant_mode" /> | |
| 46 </inputs> | |
| 47 <outputs> | |
| 48 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> | |
| 49 </outputs> | |
| 50 <tests> | |
| 51 <test> | |
| 52 </test> | |
| 53 </tests> | |
| 54 <help> | |
| 55 **What it does** | |
| 56 | |
| 57 Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data. | |
| 58 Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the | |
| 59 protein itself. We have used the HPRD_ binary interaction data to build a p-p network graph which can be explored by GEMINI. | |
| 60 | |
| 61 .. _HPRD: http://www.ncbi.nlm.nih.gov/pubmed/18988627 | |
| 62 | |
| 63 | |
| 64 @CITATION@ | |
| 65 </help> | |
| 66 <expand macro="citations"> | |
| 67 <citation type="doi">10.1093/nar/gkn892</citation><!-- HPRD citation --> | |
| 68 </expand> | |
| 69 </tool> |