# HG changeset patch
# User yating-l
# Date 1502311082 14400
# Node ID e50fc56bd10de220106d69412c27ae136f6671d8
# Parent  4c4e8941fedafce0410ed8dba57447bece4ceb0f
Uploaded

diff -r 4c4e8941feda -r e50fc56bd10d hubArchiveCreator.xml
--- a/hubArchiveCreator.xml	Mon Jul 10 17:06:11 2017 -0400
+++ b/hubArchiveCreator.xml	Wed Aug 09 16:38:02 2017 -0400
@@ -117,6 +117,10 @@
                     #end if
                     #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
                         --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment
+                        #if $f.formatChoice.bedChoice.if_index.if_index_selector == "true"
+                            #set search_index = $f.formatChoice.bedChoice.if_index.search_index
+                            #silent extra_data_dict.update({"search_index": $search_index})
+                        #end if
                         #set database = str($f.formatChoice.bedChoice.database)
                         #silent extra_data_dict.update({"database": $database})
                         #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
@@ -286,7 +290,17 @@
                                 <param name="database" type="select" label="mRNA database">
                                     <option value="NCBI" selected="true">NCBI</option>
                                     <option value="Others">Others</option>
-                                </param>
+                                </param>   
+                                <conditional name="if_index">
+                                    <param name="if_index_selector" type="select" label="Provide TRIX file for searchTrix">  
+                                        <option value="true" selected="True">Provide TRIX file</option>
+                                        <option value="false">Don't provide TRIX file</option>    
+                                    </param>
+                                    <when value="true">
+                                        <param format="txt" name="search_index" type="data" label="trix index file" />
+                                    </when>
+                                    <when value="false"></when>
+                                </conditional>
                             </when>
                         </conditional>
                         <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />