# HG changeset patch
# User fubar
# Date 1376098627 14400
# Node ID fc3b5f4ff4c48af488cd0f1d1c29d5dc7dd4ebea
# Parent  94e775b410410d3f0e2a11da7a7a5a40401a1396
fixed

diff -r 94e775b41041 -r fc3b5f4ff4c4 rgrnastar/rg_rnaStar.xml
--- a/rgrnastar/rg_rnaStar.xml	Fri Aug 09 21:34:46 2013 -0400
+++ b/rgrnastar/rg_rnaStar.xml	Fri Aug 09 21:37:07 2013 -0400
@@ -106,8 +106,7 @@
     </inputs>
 
     <outputs>
-       <data format="txt" name="output_log" label="${on_string}_{jobName}.log" from_work_dir="Log.final.out"/>
-       <data format="interval" name="chimeric_junctions" label="${on_string}_{jobName}_starchimjunc.bed" from_work_dir="Chimeric.out.junction">
+       <data format="txt" name="output_log" label="${on_string}_${jobName}_starchimjunc.bed" from_work_dir="Chimeric.out.junction">
           <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter>
           <actions>
              <conditional name="refGenomeSource.genomeSource">
@@ -127,7 +126,7 @@
              </conditional>
           </actions>
        </data>
-       <data format="bam" name="chimeric_reads" label="${on_string}_{jobName}_starmappedchim.bam" 
+       <data format="bam" name="chimeric_reads" label="${on_string}_${jobName}_starmappedchim.bam" 
                     from_work_dir="Chimeric.out.bam">
          <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter>
           <actions>
@@ -148,7 +147,7 @@
              </conditional>
           </actions>
         </data>
-        <data format="interval" name="splice_junctions" label="${on_string}_{jobName}_starsplicejunct.bed" 
+        <data format="interval" name="splice_junctions" label="${on_string}_${jobName}_starsplicejunct.bed" 
                    from_work_dir="SJ.out.tab">
           <actions>
              <conditional name="refGenomeSource.genomeSource">
@@ -168,7 +167,7 @@
              </conditional>
           </actions>
         </data>
-        <data format="bam" name="mapped_reads" label="${on_string}_{jobName}_starmapped.bam" 
+        <data format="bam" name="mapped_reads" label="${on_string}_${jobName}_starmapped.bam" 
                     from_work_dir="Aligned.out.bam">
           <actions>
              <conditional name="refGenomeSource.genomeSource">
diff -r 94e775b41041 -r fc3b5f4ff4c4 rgrnastar/tool_dependencies.xml
--- a/rgrnastar/tool_dependencies.xml	Fri Aug 09 21:34:46 2013 -0400
+++ b/rgrnastar/tool_dependencies.xml	Fri Aug 09 21:37:07 2013 -0400
@@ -6,8 +6,6 @@
                 <action type="make_directory">$INSTALL_DIR</action>
                 <action type="make_directory">$INSTALL_DIR/bin</action>
                 <action type="download_by_url" target_filename="STAR_2.3.0e.tar.gz">http://rna-star.googlecode.com/files/STAR_2.3.0e.tgz</action>
-                <action type="shell_command">cp -r ./* /tmp/test</action>                
-                <action type="shell_command">echo `ls -lt` > /tmp/lslt</action>                
                 <action type="shell_command">make</action>
                 <action type="move_file">
                     <source>STAR</source>