# HG changeset patch
# User iuc
# Date 1510251351 18000
# Node ID 4aabe53ecfe0589a117463898b71aae0f1da6c07
# Parent  8850488002dc7d60aaa63502bbead6eef47143a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0

diff -r 8850488002dc -r 4aabe53ecfe0 gemini_de_novo.xml
--- a/gemini_de_novo.xml	Tue Mar 22 21:42:54 2016 -0400
+++ b/gemini_de_novo.xml	Thu Nov 09 13:15:51 2017 -0500
@@ -11,9 +11,7 @@
 <![CDATA[
         gemini @BINARY@
 
-            #if $report.report_selector != 'all':
-                --columns "${report.columns}"
-            #end if
+            @COLUMN_SELECT@
 
             @CMDLN_SQL_FILTER_FILTER_OPTION@
 
diff -r 8850488002dc -r 4aabe53ecfe0 gemini_macros.xml
--- a/gemini_macros.xml	Tue Mar 22 21:42:54 2016 -0400
+++ b/gemini_macros.xml	Thu Nov 09 13:15:51 2017 -0500
@@ -3,6 +3,8 @@
         <requirements>
             <requirement type="package" version="0.18.1">gemini</requirement>
             <requirement type="package" version="0.2.6">tabix</requirement>
+            <!-- for conda useage -->
+            <!--requirement type="package" version="1.3.1">htslib</requirement-->
             <yield />
         </requirements>
     </xml>
@@ -63,6 +65,7 @@
                     <option value="impact_severity">impact_severity</option>
                     <option value="max_aaf_all">alternative allele frequency</option>
                 </param>
+                <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/>
             </when>
         </conditional>
     </xml>
@@ -96,6 +99,16 @@
         #end if
     </token>
 
+    <token name="@COLUMN_SELECT@">
+        #if $report.report_selector != 'all':
+            --columns "${report.columns}
+            #if str($report.extra_cols).strip()
+                #echo ','+','.join(str($report.extra_cols).split()) 
+            #end if
+            "
+        #end if
+    </token>
+
     <xml name="family">
         <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>
     </xml>
diff -r 8850488002dc -r 4aabe53ecfe0 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Mar 22 21:42:54 2016 -0400
+++ b/repository_dependencies.xml	Thu Nov 09 13:15:51 2017 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the GEMINI data manager definition to install all required annotation databases.">
-    <repository changeset_revision="345412d58d75" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="172815da3d41" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>
diff -r 8850488002dc -r 4aabe53ecfe0 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Tue Mar 22 21:42:54 2016 -0400
+++ b/tool_data_table_conf.xml.sample	Thu Nov 09 13:15:51 2017 -0500
@@ -1,5 +1,5 @@
 <tables>
-    <table name="gemini_databases" comment_char="#">
+    <table name="gemini_databases" comment_char="#" allow_duplicate_entries="False">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/gemini_databases.loc" />
     </table>