Mercurial > repos > iuc > gemini
comparison gemini_pathways.xml @ 11:53a5647e5271 draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 18 Feb 2015 11:36:37 -0500 |
| parents | 6ab82d8ca805 |
| children | 65f742e605ec |
comparison
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| 10:0f1bcedd836f | 11:53a5647e5271 |
|---|---|
| 17 > "${ outfile }" | 17 > "${ outfile }" |
| 18 ]]> | 18 ]]> |
| 19 </command> | 19 </command> |
| 20 <expand macro="stdio" /> | 20 <expand macro="stdio" /> |
| 21 <inputs> | 21 <inputs> |
| 22 <param name="infile" type="data" format="sqlite" label="GEMINI database" /> | 22 <expand macro="infile" /> |
| 23 | 23 |
| 24 <param name="ensembl" type="integer" value="68" size="5" label="Version of ensembl genes to use" | 24 <param name="ensembl" type="integer" value="68" size="5" label="Version of ensembl genes to use" |
| 25 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)"> | 25 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)"> |
| 26 <validator type="in_range" min="66" max="71"/> | 26 <validator type="in_range" min="66" max="71"/> |
| 27 </param> | 27 </param> |
| 29 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False" | 29 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False" |
| 30 label="Report only pathways with loss-of-function variants" help="(--lof)"/> | 30 label="Report only pathways with loss-of-function variants" help="(--lof)"/> |
| 31 <expand macro="annotation_dir" /> | 31 <expand macro="annotation_dir" /> |
| 32 </inputs> | 32 </inputs> |
| 33 <outputs> | 33 <outputs> |
| 34 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> | 34 <data name="outfile" format="tabular" /> |
| 35 </outputs> | 35 </outputs> |
| 36 <tests> | 36 <tests> |
| 37 <test> | 37 <test> |
| 38 </test> | 38 </test> |
| 39 </tests> | 39 </tests> |