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changeset 11:efc56ee1ade4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:23:17 -0500
parents 777ccdd1d6e4
children 05087b27692a
files picard_SortSam.xml read_group_macros.xml tool_dependencies.xml
diffstat 3 files changed, 4 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/picard_SortSam.xml	Sun Oct 11 10:46:17 2015 -0400
+++ b/picard_SortSam.xml	Wed Nov 11 12:23:17 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.0">
+<tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.1">
   <description>sort SAM/BAM dataset</description>
   <macros>
     <import>picard_macros.xml</import>
@@ -21,7 +21,6 @@
     <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate">
       <option value="coordinate" selected="True">Coordinate</option>
       <option value="queryname">Queryname</option>
-      <option value="unsorted">Unsorted</option>
     </param>
     <expand macro="VS" />
   </inputs>
@@ -56,7 +55,7 @@
 @description@
 
   SORT_ORDER=SortOrder
-  SO=SortOrder                  Sort order of output file  Required. Possible values: {unsorted, queryname, coordinate} 
+  SO=SortOrder          Sort order of output file. You can either sort by queryname or by coordinate.
  
  @more_info@
 
--- a/read_group_macros.xml	Sun Oct 11 10:46:17 2015 -0400
+++ b/read_group_macros.xml	Wed Nov 11 12:23:17 2015 -0500
@@ -121,7 +121,7 @@
         #set $rg_pg = ''
     #end if
 
-    #if str($rg_param("PI"))
+    #if $rg_param("PI") != None
         #set $rg_pi = str($rg_param("PI"))
     #else
         #set $rg_pi = ''
--- a/tool_dependencies.xml	Sun Oct 11 10:46:17 2015 -0400
+++ b/tool_dependencies.xml	Wed Nov 11 12:23:17 2015 -0500
@@ -4,6 +4,6 @@
         <repository changeset_revision="3e9c24e5325b" name="package_picard_1_136" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="R" version="3.1.2">
-        <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>