# HG changeset patch
# User rnateam
# Date 1404835189 14400
# Node ID a92d8689aa30be7572d476ebac5f8c0b254b7da9
# Parent  768a67f6ae18faf622ba0083bb9a5aac128e02c4
Uploaded

diff -r 768a67f6ae18 -r a92d8689aa30 blockclust.xml
--- 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>
diff -r 768a67f6ae18 -r a92d8689aa30 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue May 06 07:49:25 2014 -0400
+++ b/tool_dependencies.xml	Tue Jul 08 11:59:49 2014 -0400
@@ -1,22 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="6b6b5498d9a2" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="6b6b5498d9a2" 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="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="eden" version="1.1">
-        <repository changeset_revision="532625813f2e" name="package_eden_1_1" owner="rnateam" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="532625813f2e" name="package_eden_1_1" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="mcl" version="12.135">
-        <repository changeset_revision="9f59d1a59999" name="package_mcl_12_135" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="9f59d1a59999" name="package_mcl_12_135" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="blockclust_rlibs" version="1.0">
          <install version="1.0">
             <actions>
                 <action type="setup_r_environment">
-                    <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                    <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>
                     <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ape_3.0-11.tar.gz</package>