diff gemini_autosomal_recessive.xml @ 11:53a5647e5271 draft

Uploaded

--- a/gemini_autosomal_recessive.xml	Mon Aug 25 16:37:46 2014 -0400
+++ b/gemini_autosomal_recessive.xml	Wed Feb 18 11:36:37 2015 -0500
@@ -9,7 +9,7 @@
 <![CDATA[
         gemini 
 
-            #if $rec_or_dom == 'recessive':
+            #if str($rec_or_dom) == 'recessive':
                 ## start autosomal_recessive
                 autosomal_recessive
             #else:
@@ -17,13 +17,11 @@
                 autosomal_dominant
             #end if
 
-            #if $report.report_selector != 'all':
+            #if str($report.report_selector) != 'all':
                 --columns "${report.columns}"
             #end if
 
-            #if $filter.filter_selector == 'yes':
-                --filter "${filter.filter}"
-            #end if
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
 
             -d $d
             #if int($min_kindreds) > 0:
@@ -42,16 +40,16 @@
             <option value="dominant">dominant</option>
         </param>
 
-        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <expand macro="infile" />
         <expand macro="column_filter" />
         <expand macro="filter" />
         <expand macro="min_sequence_depth" />
-        <param name="min_kindreds" size="4" type="integer" value="-1" lebel="The min. number of kindreds that must have a candidate variant in a gene"
+        <param name="min_kindreds" size="4" type="integer" value="-1" label="The min. number of kindreds that must have a candidate variant in a gene"
             help="-1 means default values (--min-kindreds)" />
 
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>