changeset 7:bcd05315efc5 draft

planemo upload commit 0278da78e2822e80025c39b1bc1cd71bc4b0860f

--- a/abims_anova.xml	Mon Apr 04 08:38:43 2016 -0400
+++ b/abims_anova.xml	Mon Apr 04 08:46:20 2016 -0400
@@ -11,7 +11,7 @@
         <exit_code range="1:" level="fatal" />
     </stdio>
 
-    <command interpreter="Rscript"><![CDATA[
+    <command interpreter="Rscript">
 abims_anova.r file "$input" sampleinfo "$sampleinfo" mode "$mode" 
 condition "c('$condition_1'
 #for $i, $s in enumerate( $conditions )
@@ -19,7 +19,7 @@
 #end for
 )"
 interaction $interaction method $method threshold $threshold selection_method $selection_method sep "$sep" dec "$dec" outputdatapvalue $dataMatrixPValue outputdatafiltered $dataMatrixFiltered
-    ]]></command> 
+    </command> 
 
     <inputs>
         <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
@@ -92,7 +92,7 @@
         </test>
     </tests>
 
-    <help><![CDATA[
+    <help>
 
 .. class:: infomark
 
@@ -248,7 +248,7 @@
 
 .. image:: anova_workflow.png
 
-    ]]></help>
+    </help>
 
     <citations>
         <citation>Ronald A. Fisher in the 1930s</citation>

--- a/tool_dependencies.xml	Mon Apr 04 08:38:43 2016 -0400
+++ b/tool_dependencies.xml	Mon Apr 04 08:46:20 2016 -0400
@@ -3,7 +3,7 @@
     <package name="R" version="3.1.2">
         <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="batch" version="1.1_4">
-	<repository changeset_revision="82494b082f2f" name="package_r_batch_1_1_4" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="r-batch" version="1.1_4">
+	<repository changeset_revision="e8a964ca8656" name="package_r_batch_1_1_4" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>