# HG changeset patch
# User iuc
# Date 1539797451 14400
# Node ID 666f60a9331adc9046cb9b3d94d4f2f398ba49a7
# Parent  18f459744a975383f5426ae50b573b12eb51b72d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d

diff -r 18f459744a97 -r 666f60a9331a gemini_macros.xml
--- a/gemini_macros.xml	Thu Nov 09 13:17:45 2017 -0500
+++ b/gemini_macros.xml	Wed Oct 17 13:30:51 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>
 
diff -r 18f459744a97 -r 666f60a9331a gemini_query.xml
--- a/gemini_query.xml	Thu Nov 09 13:17:45 2017 -0500
+++ b/gemini_query.xml	Wed Oct 17 13:30:51 2018 -0400
@@ -13,13 +13,13 @@
 
             --in "${in}"
 
-            #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@
 
-            #if $sample_filter.strip():
-                --sample-filter "${sample_filter}"
-            #end if
+            #set $multiline_sql_expr = $sample_filter
+            #set $cmdln_param = "--sample-filter"
+            @MULTILN_SQL_EXPR_TO_CMDLN@
 
             $show_samples
             $show_families
@@ -35,9 +35,9 @@
             ##--format FORMAT       Format of output (JSON, TPED or default) # we will take default for the time being
             ##   --sample-delim STRING The delimiter to be used with the --show-samples option.
 
-            #if $q.strip():
-                -q "${q}"
-            #end if
+            #set $multiline_sql_expr = $q
+            #set $cmdln_param = "-q"
+            @MULTILN_SQL_EXPR_TO_CMDLN@
 
             "${ infile }"
             > "${ outfile }"