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changeset 4:ba3abde6775b draft default tip

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Uploaded
author iuc
date Thu, 15 Jan 2015 15:33:48 -0500
parents ed88ab9ead28
children
files gemini_autosomal_recessive.xml gemini_comp_hets.xml gemini_de_novo.xml gemini_macros.xml gemini_region.xml tool_dependencies.xml
diffstat 6 files changed, 15 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/gemini_autosomal_recessive.xml	Tue Jan 13 10:07:11 2015 -0500
+++ b/gemini_autosomal_recessive.xml	Thu Jan 15 15:33:48 2015 -0500
@@ -21,9 +21,7 @@
                 --columns "${report.columns}"
             #end if
 
-            #if str($filter.filter_selector) == 'yes':
-                --filter "${filter.filter}"
-            #end if
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
 
             -d $d
             #if int($min_kindreds) > 0:
--- a/gemini_comp_hets.xml	Tue Jan 13 10:07:11 2015 -0500
+++ b/gemini_comp_hets.xml	Thu Jan 15 15:33:48 2015 -0500
@@ -14,9 +14,8 @@
                 --columns "${report.columns}"
             #end if
 
-            #if $filter.filter_selector == 'yes':
-                --filter "${filter.filter}"
-            #end if
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
+
             $only_affected
             $ignore_phasing
 
--- a/gemini_de_novo.xml	Tue Jan 13 10:07:11 2015 -0500
+++ b/gemini_de_novo.xml	Thu Jan 15 15:33:48 2015 -0500
@@ -14,9 +14,8 @@
                 --columns "${report.columns}"
             #end if
 
-            #if $filter.filter_selector == 'yes':
-                --filter "${filter.filter}"
-            #end if
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
+
             -d $d
             "${ infile }"
             > "${ outfile }"
--- a/gemini_macros.xml	Tue Jan 13 10:07:11 2015 -0500
+++ b/gemini_macros.xml	Thu Jan 15 15:33:48 2015 -0500
@@ -88,11 +88,17 @@
 
     <xml name="sanitize_query">
         <sanitizer invalid_char="">
-            <valid initial="string.printable">
-            </valid>
+            <valid initial="string.printable"/>
        </sanitizer>
     </xml>
 
+    <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
+        #if str($filter.filter_selector) == 'yes' and $filter.filter:
+            #import pipes
+            --filter ${ pipes.quote( str( $filter.filter ) ) or "''" }
+        #end if
+    </token>
+
     <xml name="min_sequence_depth">
         <param name="d" type="integer" value="0" size="5" label="The minimum aligned sequence depth (genotype DP) required for each sample"
                 help="default: 0 (-d)">
--- a/gemini_region.xml	Tue Jan 13 10:07:11 2015 -0500
+++ b/gemini_region.xml	Thu Jan 15 15:33:48 2015 -0500
@@ -24,9 +24,7 @@
                 --columns "${report.columns}"
             #end if
 
-            #if $filter.filter_selector == 'yes':
-                --filter "${filter.filter}"
-            #end if
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
 
             $header
             "${ infile }"
--- a/tool_dependencies.xml	Tue Jan 13 10:07:11 2015 -0500
+++ b/tool_dependencies.xml	Thu Jan 15 15:33:48 2015 -0500
@@ -13,6 +13,6 @@
         <repository changeset_revision="fb3a854c7104" name="package_bedtools_2_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="gemini" version="0.10.0">
-        <repository changeset_revision="42c72725f879" name="package_gemini_0_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="7c5b37efe4e5" name="package_gemini_0_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>