diff data_manager/rnastar_index_builder.xml @ 4:102bdfdda10b draft

Uploaded

--- a/data_manager/rnastar_index_builder.xml	Fri Oct 03 21:59:55 2014 -0400
+++ b/data_manager/rnastar_index_builder.xml	Thu Jan 08 17:53:14 2015 -0500
@@ -4,10 +4,11 @@
         <requirement type="package" version="2.4.0d">rnastar</requirement>
     </requirements>
     <command interpreter="python">
-rnastar_index_builder.py --out_file "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" 
+rnastar_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" 
 --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" 
---data_table_name "rnastar_indexes" --out_index_path "${out_file.extra_files_path}" --runThreadN 1
+--runThreadN 1
 #if $genemodel.modelformat=="gff3":
+ --sjdbGTFchrPrefix "${genemodel.sjdbGTFchrPrefix}"
  --sjdbOverhang "${genemodel.sjdbOverhang}"
  --sjdbGTFfile "${genemodel.sjdbGTFfile}"
  --sjdbGTFtagExonParentTranscript "${genemodel.sjdbGTFtagExonParentTranscript}"
@@ -20,7 +21,9 @@
 #if $genemodel.modelformat=="None":
  --sjdbOverhang 0
 #end if
+--data_table_name "rnastar_index" 
 </command>
+
     <stdio>
         <regex match=".*" source="both" level="warning" description="stdout/err chatter:"/>
     </stdio>
@@ -50,7 +53,7 @@
                         <valid initial="string.printable"/>
                      </sanitizer>
                 </param>
-                <param type="text" name="sjdbGTFfeatureExon" value="exon_id" label="GTF feature to use as exon marker"
+                <param type="text" name="sjdbGTFfeatureExon" value="exon" label="GTF feature to use as exon marker"
                    help="GTF feature type in GTF file to be used as exons for building transcripts - use what's in your GTF">
                     <sanitizer invalid_char="">
                         <valid initial="string.printable"/>
@@ -58,7 +61,7 @@
                 </param>
                    
                 <param type="text" name="sjdbGTFtagExonParentTranscript" value="transcript_id" label="GTF feature to define for each exon's parents"
-                   help="GTF tag name to be used as exons' parents for building transcripts - use what's in your GTF">
+                   help="GTF tag name to be used as exons' parents for building transcripts - use what's in your gene model file eg parent for gff3">
                     <sanitizer invalid_char="">
                         <valid initial="string.printable"/>
                      </sanitizer>