# HG changeset patch
# User iuc
# Date 1408968457 14400
# Node ID 71dc823545955177343ea6d361a98a43b28f0d95
# Parent  4e17a332f0d815fabd125fc563dff8ef2768b995
Uploaded

diff -r 4e17a332f0d8 -r 71dc82354595 gemini_burden.xml
--- 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 }"
diff -r 4e17a332f0d8 -r 71dc82354595 gemini_macros.xml
--- 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)">
diff -r 4e17a332f0d8 -r 71dc82354595 gemini_query.xml
--- 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)"/>
diff -r 4e17a332f0d8 -r 71dc82354595 gemini_region.xml
--- 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