--- a/blockclust.xml	Tue May 06 07:49:25 2014 -0400
+++ b/blockclust.xml	Tue Jul 08 11:59:49 2014 -0400
@@ -12,10 +12,9 @@
     <command>
 
         #if str($tool_mode.operation) == "pre":
-            #set $outputdir = $tags_bed.extra_files_path
             BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed
         #elif str($tool_mode.operation) == "clust":
-            #set $outputdir = $clusters.extra_files_path
+            #set $outputdir = $clusters.files_path
             #set $accept_bed=list()
             #set $reject_bed=list()
             ## prepare annotations
@@ -67,10 +66,7 @@
             cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
             cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out
         #elif str($tool_mode.operation) == "post":
-            #set $outputdir = $clusters_bed.extra_files_path
-            BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o $outputdir;
-            cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
-            cp #echo os.path.join($outputdir, 'hclust_tree_clusters.pdf')# $cluster_hclust
+            BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o ./;
         #end if
     </command>
     <inputs>
@@ -147,10 +143,10 @@
         <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">
             <filter> tool_mode["operation"]=="clust"</filter>
         </data>
-        <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" >
+        <data format="pdf" name="cluster_dist" from_work_dir="cluster_distribution.pdf" label="BlockClust: Cluster distribution on ${on_string}" >
             <filter> tool_mode["operation"]=="post"</filter>
         </data>
-        <data format="pdf" name="cluster_hclust" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >
+        <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >
             <filter> tool_mode["operation"]=="post"</filter>
         </data>
     </outputs>