# HG changeset patch
# User fabio
# Date 1523620289 14400
# Node ID 1af09c5ec0a13db9d96ec3df9d0738b8051ec2f3
# Parent  c144495810c26ea5b5a39830cd90dff065be5c73
Uploaded 20180413

diff -r c144495810c2 -r 1af09c5ec0a1 ._.shed.yml
Binary file ._.shed.yml has changed
diff -r c144495810c2 -r 1af09c5ec0a1 ._query.py
Binary file ._query.py has changed
diff -r c144495810c2 -r 1af09c5ec0a1 ._query.xml
Binary file ._query.xml has changed
diff -r c144495810c2 -r 1af09c5ec0a1 query.py
--- a/query.py	Thu Apr 05 06:22:42 2018 -0400
+++ b/query.py	Fri Apr 13 07:51:29 2018 -0400
@@ -35,6 +35,7 @@
     payload["search_mode"] = str(options.search);
     payload["exact_algorithm"] = int(options.exact);
     payload["search_threshold"] = float(options.sthreshold);
+    payload["sort"] = int(options.sortcontrol);
     # set the content type to application/json
     headers = {'Content-type': 'application/json'};
 
@@ -187,6 +188,8 @@
                     action="store", dest="treeid", help="the id of the tree that will be queried");
     parser.add_option("-t", "--sthreshold", type="float",
                     action="store", dest="sthreshold", help="threshold applied to the search algrithm");
+    parser.add_option("-z", "--sort", type="int", default=1,
+                    action="store", dest="sortcontrol", help="boolean required to sort the result");
     parser.add_option("-o", "--outputdir", type="string", default="output",
                     action="store", dest="outputdir", help="output directory (collection) path");
     parser.add_option("-r", "--errorfile", type="string", default="error_txt",
diff -r c144495810c2 -r 1af09c5ec0a1 query.xml
--- a/query.xml	Thu Apr 05 06:22:42 2018 -0400
+++ b/query.xml	Fri Apr 13 07:51:29 2018 -0400
@@ -12,6 +12,7 @@
     --tree 1
     --search 'rrr'
     --sthreshold ${sthreshold}
+    --sort ${sortcontrol}
     --exact 0
     
     #if $conditional_input.inputtype == '0':
@@ -42,6 +43,7 @@
             </when>
         </conditional>            
         <param name="sthreshold" size="3" type="float" value="0.7" min="0.0" max="1.0" label="Search threshold" help="This threshold controls the specificity. Lower values will produce more hits to the query. Higher values are more stringent and will produce fewer hits." />
+        <param name="sortcontrol" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Sort the result by the number of hits per transcript." />
     </inputs>
     <outputs>
         <collection name="output_collect" type="list" label="BloomTree Manager - Query result collection">