diff data_manager/rnastar_index_builder.xml @ 5:503097df1670 draft

Uploaded

--- a/data_manager/rnastar_index_builder.xml	Thu Jan 08 17:53:14 2015 -0500
+++ b/data_manager/rnastar_index_builder.xml	Fri Jan 09 22:38:21 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="rnastar_index_builder_data_manager" name="rnastar index" tool_type="manage_data" version="0.0.1">
+<tool id="rnastar_index_builder_data_manager" name="rnastar index" tool_type="manage_data" version="0.0.2">
     <description>builder</description>
     <requirements>
         <requirement type="package" version="2.4.0d">rnastar</requirement>
@@ -23,18 +23,12 @@
 #end if
 --data_table_name "rnastar_index" 
 </command>
-
-    <stdio>
-        <regex match=".*" source="both" level="warning" description="stdout/err chatter:"/>
-    </stdio>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta"/>
         </param>
         <param type="text" name="sequence_name" value="" label="Informative name for sequence index" />
         <param type="text" name="sequence_id" value="" label="ID for sequence index" />
-
-
         <conditional name="genemodel">
             <param name="modelformat" type="select" 
                label="Choose the format of gene model data from your history - bed or gff3"
@@ -68,14 +62,14 @@
                 </param>
                    
                 <param type="integer" name="sjdbOverhang" value="100" label="Splice junction overhang. If=0, splice junction database NOT used"
-                help="int>=0: length of the donor/acceptor sequence on each side, (mate_length - 1)" />
+                help="integer length of the donor/acceptor sequence on each side, (mate_length - 1)" />
                 
             </when>
             <when value='bed'>
                 <param type="data" format="bed" name="sjdbFileChrStartEnd" value="" label="Introns as a tabular bed (chr,start,end,strand) file matching the input genome"
                    help="Required if you want to index splice junctions during index generation." />
                 <param type="integer" name="sjdbOverhang" value="100" label="Splice junction overhang. If=0, splice junction database NOT used"
-                help="int>=0: length of the donor/acceptor sequence on each side, (mate_length - 1)" />
+                help="integer length of the donor/acceptor sequence on each side, (mate_length - 1)" />
            </when>
             <when value='None'>
             </when>