diff data_manager/rnastar_index_builder.xml @ 6:f9d8dc8c2152 draft

Uploaded

--- a/data_manager/rnastar_index_builder.xml	Fri Jan 09 22:38:21 2015 -0500
+++ b/data_manager/rnastar_index_builder.xml	Fri Jan 09 23:16:54 2015 -0500
@@ -22,7 +22,7 @@
  --sjdbOverhang 0
 #end if
 --data_table_name "rnastar_index" 
-</command>
+    </command>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta"/>
@@ -35,7 +35,7 @@
                help="This will be the source of splice junction indexing if required">
               <option value="gff3"  selected="true">gff3,gtf</option>
               <option value="bed">BED - tabular chr,start,end,strand</option>
-              <option value="None" >None - no splice junction index</option>
+              <option value="None">None - no splice junction index</option>
              </param>
              <when value="gff3">
                 <param type="data" format="gff3,gff" name="sjdbGTFfile" value="" label="Gene model - must be gff3 or compatible and must match the input genome"
@@ -71,8 +71,8 @@
                 <param type="integer" name="sjdbOverhang" value="100" label="Splice junction overhang. If=0, splice junction database NOT used"
                 help="integer length of the donor/acceptor sequence on each side, (mate_length - 1)" />
            </when>
-            <when value='None'>
-            </when>
+           <when value='None'>
+           </when>
         </conditional>
     </inputs>
     <outputs>
@@ -82,6 +82,7 @@
 
 .. class:: infomark
 
+<![CDATA[
 *What it does*
 
 This is a Galaxy datamanager for the rna STAR gap-aware RNA aligner.
@@ -117,6 +118,6 @@
     Alex
 
 **Notice:** If you leave name, description, or id blank, it will be generated automatically. 
-
+]]>
     </help>
 </tool>