Mercurial > repos > iuc > gemini_de_novo

diff gemini_macros.xml @ 2:4aabe53ecfe0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author iuc
date Thu, 09 Nov 2017 13:15:51 -0500
parents 8850488002dc
children d5b01cc263be
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--- 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>