diff gemini_macros.xml @ 4:93a391b4602c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313

--- a/gemini_macros.xml	Wed Oct 17 13:27:38 2018 -0400
+++ b/gemini_macros.xml	Fri Dec 14 12:48:41 2018 -0500
@@ -1,7 +1,12 @@
 <macros>
+    <!-- gemini version to be used -->
+    <token name="@VERSION@">0.18.1</token>
+    <!-- minimal annotation files version required by this version of gemini -->
+    <token name="@DB_VERSION@">181</token>
+
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.18.1">gemini</requirement>
+            <requirement type="package" version="@VERSION@">gemini</requirement>
             <requirement type="package" version="0.2.6">tabix</requirement>
             <!-- for conda useage -->
             <!--requirement type="package" version="1.3.1">htslib</requirement-->
@@ -23,9 +28,10 @@
     </xml>
 
     <xml name="annotation_dir">
-        <param name="annotation_databases" type="select" optional="True" label="Choose a gemini annotation database">
-            <options from_data_table="gemini_databases">
+        <param name="annotation_databases" type="select" label="Choose a gemini annotation source">
+            <options from_data_table="gemini_versioned_databases">
                 <filter type="sort_by" column="0" />
+                <filter type="static_value" column="2" value="@DB_VERSION@" />
             </options>
         </param>
     </xml>
@@ -97,6 +103,12 @@
        </sanitizer>
     </xml>
 
+    <token name="@PROVIDE_ANNO_DATA@"><![CDATA[
+        mkdir gemini &&
+        ln -s "${annotation_databases.fields.path}/gemini/data" gemini/data &&
+        export GEMINI_CONFIG="${annotation_databases.fields.path}" &&
+    ]]></token>
+
     <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
         #set $sql_expr = str($multiline_sql_expr).strip()
         #if str($sql_expr):
@@ -153,7 +165,6 @@
     <xml name="gt_pl_max">
         <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" />
     </xml>
-    <token name="@VERSION@">0.18.1</token>
 
     <xml name="citations">
         <citations>