# HG changeset patch
# User iuc
# Date 1539797388 14400
# Node ID d46017ddbf946eb0ae3199ae9ea19d3740837bc1
# Parent  bc66ebfd4159f4c1e96f9c1cdca5200a18c825db
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d

diff -r bc66ebfd4159 -r d46017ddbf94 gemini_gene_wise.xml
--- a/gemini_gene_wise.xml	Thu Nov 09 13:16:54 2017 -0500
+++ b/gemini_gene_wise.xml	Wed Oct 17 13:29:48 2018 -0400
@@ -16,9 +16,9 @@
                 --min_filters $min_filters
             #end if
 
-            #if $gt_filter.strip():
-                --gt-filter "${gt_filter}"
-            #end if
+            #set $multiline_sql_expr = $gt_filter
+            #set $cmdln_param = "--gt-filter"
+            @MULTILN_SQL_EXPR_TO_CMDLN@
 
             @COLUMN_SELECT@
 
diff -r bc66ebfd4159 -r d46017ddbf94 gemini_macros.xml
--- a/gemini_macros.xml	Thu Nov 09 13:16:54 2017 -0500
+++ b/gemini_macros.xml	Wed Oct 17 13:29:48 2018 -0400
@@ -88,14 +88,28 @@
 
     <xml name="sanitize_query">
         <sanitizer invalid_char="">
-            <valid initial="string.printable"/>
+            <valid initial="string.printable">
+                <remove value="&apos;" />
+            </valid>
+            <mapping initial="none">
+                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
+            </mapping>
        </sanitizer>
     </xml>
 
+    <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
+        #set $sql_expr = str($multiline_sql_expr).strip()
+        #if str($sql_expr):
+            #set $sql_expr = $sql_expr.replace('\r\n', '\n')
+            #set $sql_expr = $sql_expr.replace('\r', '\n')
+            #set $sql_expr = $sql_expr.replace('\\\n', ' ')
+            $cmdln_param '$sql_expr'
+        #end if
+    </token>
+
     <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
         #if str($filter.filter_selector) == 'yes' and $filter.filter:
-            #import pipes
-            --filter ${ pipes.quote( str( $filter.filter ) ) or "''" }
+            --filter '${ str( $filter.filter ) }'
         #end if
     </token>