Mercurial > repos > iuc > data_manager_snpsift_dbnsfp

diff data_manager/data_manager_snpsift_dbnsfp.xml @ 3:0e9624bcd707 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit de422632b9310905f8e9d44faee9ff768752968f
author iuc
date Mon, 31 Oct 2016 08:13:28 -0400
parents d57ebdd39f0f
children 47f276ffcbfc
line wrap: on
line diff
--- a/data_manager/data_manager_snpsift_dbnsfp.xml	Fri Jun 10 08:25:06 2016 -0400
+++ b/data_manager/data_manager_snpsift_dbnsfp.xml	Mon Oct 31 08:13:28 2016 -0400
@@ -4,30 +4,30 @@
         <requirement type="package" version="0.8.3">pysam</requirement>
     </requirements>
     <stdio>
-        <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
-        <exit_code range="1:"  level="fatal"   description="Error" />
+        <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
+        <exit_code range="1:" level="fatal" description="Error" />
     </stdio>
-    <command interpreter="python">
-        #import re
-        data_manager_snpsift_dbnsfp.py 
+    <command><![CDATA[
+        python '$__tool_directory__/data_manager_snpsift_dbnsfp.py' 
         #if $db.src == 'softgenetics':
-            --softgenetics "$db.softgenetics_name"
+            --softgenetics '$db.softgenetics_name'
         #elif $db.src == 'history':
             #if $db.snpsiftdbnsfp.ext == 'snpsiftdbnsfp':
                 #import os.path
-                --snpsiftdbnsfp "$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)"
+                --snpsiftdbnsfp '$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)'
             #else 
-                --dbnsfp_tabular "$db.snpsiftdbnsfp"
+                --dbnsfp_tabular '$db.snpsiftdbnsfp'
             #end if
-            --db_name "$db.db_name"
+            --db_name '$db.db_name'
             #if str($db.dbkey).strip() != '': 
-                --dbkey "$db.dbkey" 
+                --dbkey '$db.dbkey'
             #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?':
-                --dbkey "$db.snpsiftdbnsfp.metadata.dbkey" 
+                --dbkey '$db.snpsiftdbnsfp.metadata.dbkey' 
             #end if
         #end if
-        "$out_file"
-        </command>
+        '$out_file'
+        ]]>
+    </command>
     <inputs>
         <conditional name="db">
             <param name="src" type="select" label="Source for dbNSFP file">