Mercurial > repos > jjohnson > snpeff
changeset 10:39cb913568ec
Do not select any annotations by default
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 10 Dec 2013 14:28:37 -0600 |
| parents | f981ba577f2b |
| children | c5288d5a446e |
| files | snpEff.xml |
| diffstat | 1 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/snpEff.xml Fri Nov 29 17:13:33 2013 -0600 +++ b/snpEff.xml Tue Dec 10 14:28:37 2013 -0600 @@ -54,9 +54,9 @@ #elif $snpDb.genomeSrc == 'history': -dataDir ${snpDb.snpeff_db.extra_files_path} #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': - #set annotations = [' '] + $snpDb.extra_annotations.__str__.split(',') + #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',') #echo " " - #echo ' -'.join($annotations) + #echo ' -'.join($xannotations) #end if #if $snpDb.regulation and $snpDb.regulation.__str__ != '': -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# @@ -174,12 +174,12 @@ <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option> - <option value="-canon" selected="true">Only use canonical transcripts</option> + <option value="-canon">Only use canonical transcripts</option> <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option> - <option value="-lof" selected="true">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option> + <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option> <option value="-oicr">Add OICR tag in VCF file</option> - <option value="-onlyReg" selected="true">Only use regulation tracks</option> + <option value="-onlyReg">Only use regulation tracks</option> <option value="-sequenceOntolgy">Use Sequence Ontolgy terms.</option> </param> <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>