Mercurial > repos > iuc > gemini
view gemini_pathways.xml @ 1:d3c4d0208bb2 draft
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author | iuc |
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date | Wed, 27 Aug 2014 02:26:19 -0400 |
parents | 720cbfb4190d |
children | 93bb0cfacefb |
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<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> <description>Map genes and variants to KEGG pathways</description> <expand macro="requirements" /> <expand macro="version_command" /> <macros> <import>gemini_macros.xml</import> <token name="@BINARY@">pathways</token> </macros> <command> <![CDATA[ gemini --annotation-dir ${annotation_databases.fields.path} @BINARY@ -v $ensembl $lof "${ infile }" > "${ outfile }" ]]> </command> <expand macro="stdio" /> <inputs> <param name="infile" type="data" format="sqlite" label="GEMINI database" /> <param name="ensembl" type="integer" value="68" size="5" label="Version of ensembl genes to use" help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)"> <validator type="in_range" min="66" max="71"/> </param> <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False" label="Report only pathways with loss-of-function variants" help="(--lof)"/> <expand macro="annotation_dir" /> </inputs> <outputs> <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> </outputs> <tests> <test> </test> </tests> <help> **What it does** Mapping genes to biological pathways is useful in understanding the function/role played by a gene. Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases. We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation. This requires your VCF be annotated with either snpEff/VEP. @CITATION@ </help> <expand macro="citations"/> </tool>