Mercurial > repos > iuc > gemini
changeset 8:71dc82354595 draft
Uploaded
| author | iuc |
|---|---|
| date | Mon, 25 Aug 2014 08:07:37 -0400 |
| parents | 4e17a332f0d8 |
| children | fc853d53532c |
| files | gemini_burden.xml gemini_macros.xml gemini_query.xml gemini_region.xml |
| diffstat | 4 files changed, 23 insertions(+), 8 deletions(-) [+] |
line wrap: on
line diff
--- a/gemini_burden.xml Mon Aug 25 04:25:41 2014 -0400 +++ b/gemini_burden.xml Mon Aug 25 08:07:37 2014 -0400 @@ -15,10 +15,10 @@ $nonsynonymous $calpha --permutations $permutations - #if float($min_aaf) >= 0.0: + #if float( str($min_aaf) ) >= 0.0: --min-aaf $min_aaf #end if - #if float($max_aaf) >= 0.0: + #if float( str($max_aaf) ) >= 0.0: --max-aaf $max_aaf #end if "${ infile }"
--- a/gemini_macros.xml Mon Aug 25 04:25:41 2014 -0400 +++ b/gemini_macros.xml Mon Aug 25 08:07:37 2014 -0400 @@ -84,11 +84,20 @@ </param> <when value="no"/> <when value="yes"> - <param name="filter" type="text" label="Contraints in SQL syntax" help="Conditions applied here will become WHERE clauses in the query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'. (--filter)" /> + <param name="filter" type="text" size="20" label="Contraints in SQL syntax" help="Conditions applied here will become WHERE clauses in the query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'. (--filter)"> + <expand macro="sanitize_query" /> + </param> </when> </conditional> </xml> + <xml name="sanitize_query"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + </valid> + </sanitizer> + </xml> + <xml name="min_sequence_depth"> <param name="d" type="integer" value="0" size="5" label="The minimum aligned sequence depth (genotype DP) required for each sample" help="default: 0 (-d)">
--- a/gemini_query.xml Mon Aug 25 04:25:41 2014 -0400 +++ b/gemini_query.xml Mon Aug 25 08:07:37 2014 -0400 @@ -51,9 +51,15 @@ <inputs> <param name="infile" type="data" format="sqlite" label="GEMINI database" /> - <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)"/> - <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)"/> - <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table" help="(--sample-filter)"/> + <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)"> + <expand macro="sanitize_query" /> + </param> + <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)"> + <expand macro="sanitize_query" /> + </param> + <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table" help="(--sample-filter)"> + <expand macro="sanitize_query" /> + </param> <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False" label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/>
--- a/gemini_region.xml Mon Aug 25 04:25:41 2014 -0400 +++ b/gemini_region.xml Mon Aug 25 08:07:37 2014 -0400 @@ -11,11 +11,11 @@ gemini @BINARY@ #if $region.region_selector == '--reg': - #if "${region.region}" == '' + #if str(${region.region}) != '': --reg "${region.region}" #end if #else: - #if "${region.gene}" != '': + #if str(${region.gene}) != '': --gene "${region.gene}" #end if #end if