Mercurial > repos > iuc > gemini_interactions
diff gemini_interactions.xml @ 0:527c8e4a356f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
| author | iuc |
|---|---|
| date | Thu, 18 Feb 2016 08:52:47 -0500 |
| parents | |
| children | a6d326ffbb72 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gemini_interactions.xml Thu Feb 18 08:52:47 2016 -0500 @@ -0,0 +1,116 @@ +<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> + <description>Find genes among variants that are interacting partners</description> + <macros> + <import>gemini_macros.xml</import> + <token name="@BINARY@">interactions</token> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + gemini + #if $annotation_databases: + --annotation-dir "${annotation_databases.fields.path}" + #end if + + #if $gene.gene_selector == 'lof': + ## lof interactions is a separate program + lof_interactions + #else: + ## use normal gemini interactions program + @BINARY@ + -g "${gene.gene}" + #end if + + -r "${radius}" + $variant_mode + "${ infile }" + > "${ outfile }" +]]> + </command> + <inputs> + <expand macro="infile" /> + + <conditional name="gene"> + <param name="gene_selector" type="select" label="Studying" help=""> + <option value="gene">Interesting gene</option> + <option value="lof">All loss-of-function variants</option> + </param> + <when value="gene"> + <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" /> + </when> + <when value="lof"/> + </conditional> + <expand macro="annotation_dir" /> + <expand macro="radius" /> + <expand macro="variant_mode" /> + </inputs> + <outputs> + <data name="outfile" format="tabular" /> + </outputs> + <tests> + <test> + <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" /> + <param name="gene" value="CTBP2" /> + <param name="radius" value="5" /> + <output name="outfile" file="gemini_interactions_result.tabular" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data. +Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the +protein itself. We have used the HPRD_ binary interaction data to build a p-p network graph which can be explored by GEMINI. + +.. _HPRD: http://www.ncbi.nlm.nih.gov/pubmed/18988627 + +**Details** + +*interactions: Find genes among variants that are interacting partners.* + +Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data. Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the protein itself. We have used the HPRD binary interaction data to build a p-p network graph which can be explored by GEMINI. + +**Examples** + +EXAMPLE with setting -g CTBP2 and -r 3:: + + sample gene order_of_interaction interacting_gene + M128215 CTBP2 0_order: CTBP2 + M128215 CTBP2 1_order: RAI2 + M128215 CTBP2 2_order: RB1 + M128215 CTBP2 3_order: TGM2,NOTCH2NL + +Return CTBP2 (-g) interacting gene variants till the third order (-r) + +EXAMPLE lof_interactions (use this option to restrict your analysis to only LoF variants); lof_interactions and -r 3:: + + sample lof_gene order_of_interaction interacting_gene + M128215 TGM2 1_order: RB1 + M128215 TGM2 2_order: none + M128215 TGM2 3_order: NOTCH2NL,CTBP2 + +Meaning to say return all LoF gene TGM2 (in sample M128215) interacting partners to a 3rd order of interaction. + +EXAMPLE --var. An extended variant information (chrom, start, end etc.) for the interacting gene may be achieved with the –var option for both the interactions and the lof_interactions. Settings '-g CTBP2', '-r 3' and '--var':: + + sample gene order_of_interaction interacting_gene var_id chrom start end impact biotype in_dbsnp clinvar_sig clinvar_disease_name aaf_1kg_all aaf_esp_all + M128215 CTBP2 0 CTBP2 5 chr10 126678091 126678092 stop_gain protein_coding 1 None None None None + M128215 CTBP2 1 RAI2 9 chrX 17819376 17819377 non_syn_coding protein_coding 1 None None 1 0.000473 + M128215 CTBP2 2 RB1 7 chr13 48873834 48873835 upstream protein_coding 1 None None 0.94 None + M128215 CTBP2 3 NOTCH2NL 1 chr1 145273344 145273345 non_syn_coding protein_coding 1 None None None None + M128215 CTBP2 3 TGM2 8 chr20 36779423 36779424 stop_gain protein_coding 0 None None None None + +EXAMPLE with the following settings; '-r 3', '--var':: + + sample lof_gene order_of_interaction interacting_gene var_id chrom start end impact biotype in_dbsnp clinvar_sig clinvar_disease_name aaf_1kg_all aaf_esp_all + M128215 TGM2 1 RB1 7 chr13 48873834 48873835 upstream protein_coding 1 None None 0.94 None + M128215 TGM2 3 NOTCH2NL 1 chr1 145273344 145273345 non_syn_coding protein_coding 1 None None None None + M128215 TGM2 3 CTBP2 5 chr10 126678091 126678092 stop_gain protein_coding 1 None None None None + + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1093/nar/gkn892</citation><!-- HPRD citation --> + </expand> +</tool>