diff rsem_prepare_reference.xml @ 3:59459de65740

mv RSEM datatypes to separate repository, remove samtools dependency

--- a/rsem_prepare_reference.xml	Fri Feb 07 07:34:29 2014 -0600
+++ b/rsem_prepare_reference.xml	Mon Mar 10 07:19:56 2014 -0500
@@ -5,6 +5,7 @@
     <requirement type="package" version="1.0.0">bowtie</requirement>
   </requirements>
   <command>
+    echo $reference_name " " | tee $reference_file &amp;&amp;
     mkdir $reference_file.extra_files_path &amp;&amp; 
     cd $reference_file.extra_files_path &amp;&amp; 
     rsem-prepare-reference 
@@ -31,6 +32,7 @@
       $reference.reference_fasta_file
     #end if
     $reference_name
+    > ${reference_name}.log
   </command>
   <inputs>
     <conditional name="reference">
@@ -61,7 +63,7 @@
       </help>
     </param>
     <param name="reference_name" type="text" value="rsem_ref_name" label="reference name">
-      <help>A one work name for this RSEM reference containing only letters, digits, and underscore characters</help>
+      <help>A one word name for this RSEM reference containing only letters, digits, and underscore characters</help>
       <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator>
     </param>
     <conditional name="polya">