Mercurial > repos > iuc > gemini
comparison gemini_pathways.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>Map genes and variants to KEGG pathways</description> | |
| 3 <expand macro="requirements" /> | |
| 4 <expand macro="version_command" /> | |
| 5 <macros> | |
| 6 <import>gemini_macros.xml</import> | |
| 7 <token name="@BINARY@">pathways</token> | |
| 8 </macros> | |
| 9 <command> | |
| 10 <![CDATA[ | |
| 11 gemini @BINARY@ | |
| 12 -v $ensembl | |
| 13 $lof | |
| 14 "${ infile }" | |
| 15 > "${ outfile }" | |
| 16 ]]> | |
| 17 </command> | |
| 18 <expand macro="stdio" /> | |
| 19 <inputs> | |
| 20 <param name="infile" type="data" format="sqlite" label="GEMINI database" /> | |
| 21 | |
| 22 <param name="ensemble" type="integer" value="68" size="5" label="Version of ensembl genes to use" | |
| 23 help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)"> | |
| 24 <validator type="in_range" min="66" max="71"/> | |
| 25 </param> | |
| 26 | |
| 27 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False" | |
| 28 label="Report only pathways with loss-of-function variants" help="(--lof)"/> | |
| 29 | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 <test> | |
| 36 </test> | |
| 37 </tests> | |
| 38 <help> | |
| 39 **What it does** | |
| 40 | |
| 41 Mapping genes to biological pathways is useful in understanding the function/role played by a gene. | |
| 42 Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases. | |
| 43 We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation. | |
| 44 | |
| 45 This requires your VCF be annotated with either snpEff/VEP. | |
| 46 | |
| 47 @CITATION@ | |
| 48 </help> | |
| 49 <expand macro="citations"/> | |
| 50 </tool> |