--- a/blockclust.xml	Sun Sep 21 23:00:44 2014 -0400
+++ b/blockclust.xml	Tue Feb 03 05:49:47 2015 -0500
@@ -3,13 +3,14 @@
     <requirements>
         <requirement type="package" version="1.0">blockclust</requirement>
         <requirement type="package" version="1.1">eden</requirement>
-        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
+        <requirement type="package" version="3.0.3">R</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
         <requirement type="package" version="12.135">mcl</requirement>
         <requirement type="package" version="1.0">blockclust_rlibs</requirement>
     </requirements>
     <version_command>echo '1.0'</version_command>
     <command>
+<![CDATA[
         #if str($tool_mode.operation) == "pre":
             BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed
         #elif str($tool_mode.operation) == "clust":
@@ -49,7 +50,7 @@
             -o $outputdir
             #if $tool_mode.nochr:
                 -nochr
-            #end if          
+            #end if
             #if str($tool_mode.pred.enable_pred) == "yes":
                 -p
                 -pm $tool_mode.pred.pred_mode
@@ -69,6 +70,7 @@
         #elif str($tool_mode.operation) == "post":
             BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -rfam \$BLOCKCLUST_DATA_PATH/rfam_map.txt -o ./;
         #end if
+]]>
     </command>
     <inputs>
         <conditional name="tool_mode">
@@ -127,7 +129,7 @@
         <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based predictions BED on ${on_string}">
             <filter>
             ((
-                tool_mode["operation"] == 'clust' and 
+                tool_mode["operation"] == 'clust' and
                 tool_mode["pred"]["enable_pred"] == "yes" and
                 tool_mode["pred"]["pred_mode"] == "model_based"
              ))
@@ -136,7 +138,7 @@
         <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbor predictions BED on ${on_string}">
             <filter>
             ((
-                tool_mode["operation"] == 'clust' and 
+                tool_mode["operation"] == 'clust' and
                 tool_mode["pred"]["enable_pred"] == "yes" and
                 tool_mode["pred"]["pred_mode"] == "nearest_neighbour"
              ))
@@ -153,18 +155,19 @@
         </data>
     </outputs>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
-**What it does** 
+**What it does**
 
-BlockClust is an efficient approach to detect transcripts with similar 
+BlockClust is an efficient approach to detect transcripts with similar
 processing patterns. We propose a novel way to encode expression profiles
-in compact discrete structures, which can then be processed using 
-fast graph-kernel techniques. BlockClust allows both clustering and 
+in compact discrete structures, which can then be processed using
+fast graph-kernel techniques. BlockClust allows both clustering and
 classification of small non-coding RNAs.
 
-BlockClust runs in three operating modes: 
+BlockClust runs in three operating modes:
 
 1) Pre-processing - converts given mapped reads (BAM) into BED file of tags
 
@@ -207,10 +210,11 @@
 
 ------
 
-**References** 
+**References**
 
 Pavankumar Videm, Dominic Rose, Fabrizio Costa, and Rolf Backofen. "BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles." Bioinformatics 30, no. 12 (2014): i274-i282.
 
 
+]]>
     </help>
 </tool>

--- a/tool_dependencies.xml	Sun Sep 21 23:00:44 2014 -0400
+++ b/tool_dependencies.xml	Tue Feb 03 05:49:47 2015 -0500
@@ -3,8 +3,8 @@
     <package name="samtools" version="0.1.19">
         <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="R_3_0_1" version="3.0.1">
-        <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="R" version="3.0.3">
+        <repository changeset_revision="f386d7431fe0" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="eden" version="1.1">
         <repository changeset_revision="8087eef83c35" name="package_eden_1_1" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
@@ -16,8 +16,8 @@
          <install version="1.0">
             <actions>
                 <action type="setup_r_environment">
-                    <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="R_3_0_1" version="3.0.1" />
+                    <repository changeset_revision="f386d7431fe0" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.0.3" />
                     </repository>
                     <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ape_3.0-11.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/plyr_1.8.tar.gz</package>
@@ -57,7 +57,7 @@
                 <action type="move_file">
                     <source>filterKnownBlockGroups.pl</source>
                     <destination>$INSTALL_DIR/bin</destination>
-                </action>                
+                </action>
                 <action type="move_file">
                     <source>perf</source>
                     <destination>$INSTALL_DIR/bin</destination>
@@ -98,7 +98,7 @@
             </actions>
         </install>
         <readme>
-	
+
         </readme>
     </package>
 </tool_dependency>