--- a/defuse.xml	Wed Oct 18 16:55:57 2017 -0400
+++ b/defuse.xml	Thu Oct 19 10:05:54 2017 -0400
@@ -9,27 +9,28 @@
   <command><![CDATA[
     #if $defuse_out.__str__ != 'None':
         ## ln to output_dir in from_work_dir
-        mkdir -p $defuse_out.dataset.extra_files_path &&
-        ln -s $defuse_out.dataset.extra_files_path  output_dir &&
+        mkdir -p $defuse_out.files_path &&
+        ln -s $defuse_out.files_path  output_dir &&
     #else
       mkdir -p output_dir &&
     #end if
     ## Put executable paths in config file
     $__tool_directory__/config_sub.sh $defuse_config output_dir/defuse.cfg &&
     ## copy config to output
-    cp defuse.cfg $config_txt &&
+    cp output_dir/defuse.cfg $config_txt &&
     ## make a data_dir  and ln -s the input fastq
     mkdir -p data_dir &&
     ln -s "$left_pairendreads" data_dir/reads_1.fastq &&
     ln -s "$right_pairendreads" data_dir/reads_2.fastq &&
     ## run 
-    perl defuse_run.pl --name "$library_name" --config defuse.cfg  -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p \$GALAXY_SLOTS &&
+    DATASET_DIRECTORY=`grep '^dataset_directory' output_dir/defuse.cfg | awk '{print \$NF}'` &&
+    defuse_run.pl --name "$library_name" --config output_dir/defuse.cfg --dataset \$DATASET_DIRECTORY -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p \$GALAXY_SLOTS &&
     grep -v cluster_id  output_dir/results.filtered.tsv | awk '{print $1}' > cluster_id_list && 
     get_fusion_fastq.pl --list cluster_id_list --output output_dir --fastq1 results.fusions_1.fq --fastq2 results.fusions_2.fq && 
     cp output_dir/results.* .  &&
-    cp `find output_dir -name defuse.log` $defuse_log 
+    cp `find -L output_dir -name defuse.log` $defuse_log 
     #if $defuse_out.__str__ != 'None':
-        && $__tool_directory__/make_html.sh $defuse_out $defuse_out.dataset.extra_files_path
+        && $__tool_directory__/make_html.sh $defuse_out $defuse_out.files_path
     #end if
   ]]></command>
  <inputs>
@@ -110,8 +111,6 @@
   <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 
          help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 
                but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
-  <param name="breakpoints_bam" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/>
-  <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
  </inputs>
  <outputs>
   <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>