diff bwa_macros.xml @ 6:09a7281d24c5 draft

planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

--- a/bwa_macros.xml	Tue Jul 21 13:51:02 2015 -0400
+++ b/bwa_macros.xml	Tue Jul 21 14:12:49 2015 -0400
@@ -14,7 +14,51 @@
       #set $rg_string += $format_read_group("\tPI:", $rg_pi)
       #set $rg_string += $format_read_group("\tPU:", $rg_pu)
   </token>
-    
+
+  <xml name="stdio">
+      <stdio>
+          <exit_code range="1:" />
+          <exit_code range=":-1" />
+          <regex match="Error:" />
+          <regex match="Exception:" />
+      </stdio>
+  </xml>
+
+  <macro name="dbKeyActionsBwa">
+    <expand macro="dbKeyActions">
+      <option type="from_data_table" name="bwa_indexes" column="1" offset="0">
+        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+        <filter type="param_value" ref="reference_source.ref_file" column="0"/>
+      </option>
+    </expand>
+  </macro>
+
+  <macro name="dbKeyActionsBwaMem">
+    <expand macro="dbKeyActions">
+      <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0">
+        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+        <filter type="param_value" ref="reference_source.ref_file" column="0"/>
+      </option>
+    </expand>
+  </macro>
+
+  <macro name="dbKeyActions">
+      <actions>
+          <conditional name="reference_source.reference_source_selector">
+              <when value="cached">
+                  <action type="metadata" name="dbkey">
+                      <yield />
+                  </action>
+              </when>
+              <when value="history">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
+                  </action>
+              </when>
+          </conditional>
+      </actions>
+  </macro>
+
   <token name="@RG@">
 -----