# HG changeset patch
# User iuc
# Date 1566049101 14400
# Node ID 41929aa1e7f360af38240e5fe07374093da979a4
# Parent  d82339e37e8e73dcb846fc1088fb67498a6a63f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f"

diff -r d82339e37e8e -r 41929aa1e7f3 macros.xml
--- a/macros.xml	Thu Aug 15 01:54:13 2019 -0400
+++ b/macros.xml	Sat Aug 17 09:38:21 2019 -0400
@@ -21,7 +21,7 @@
         </requirements>
     </xml>
 
-    <xml name="index_selection" token_with_gene_model="1">
+    <xml name="index_selection" token_with_gene_model="0">
         <param argument="--genomeDir" name="genomeDir" type="select"
         label="Select reference genome"
         help="If your genome of interest is not listed, contact the Galaxy team">
@@ -127,15 +127,15 @@
                     <param name="GTFselect" type="select"
                            label="Reference genome with or without an annotation"
                            help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions.">
-                        <option value="without-gtf">use genome reference with builtin gene-model</option>
-                        <option value="with-gtf">use genome reference without builtin gene-model</option>
+                        <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
+                        <option value="with-gtf">use genome reference with builtin gene-model</option>
                     </param>
                     <when value="with-gtf">
-                        <expand macro="index_selection" with_gene_model="0" />
+                        <expand macro="index_selection" with_gene_model="1" />
                         <expand macro="@SJDBOPTIONS@" />
                     </when>
                     <when value="without-gtf">
-                        <expand macro="index_selection" with_gene_model="1" />
+                        <expand macro="index_selection" with_gene_model="0" />
                     </when>
                 </conditional>
             </when>
diff -r d82339e37e8e -r 41929aa1e7f3 rg_rnaStar.xml
--- a/rg_rnaStar.xml	Thu Aug 15 01:54:13 2019 -0400
+++ b/rg_rnaStar.xml	Sat Aug 17 09:38:21 2019 -0400
@@ -525,7 +525,7 @@
                 <param name="geneSource" value="indexed" />
                 <conditional name="GTFconditional">
                     <param name="GTFselect" value="with-gtf" />
-                    <param name="genomeDir" value="000" />
+                    <param name="genomeDir" value="001" />
                 </conditional>
             </conditional>
             <section name="oformat">
@@ -765,7 +765,7 @@
                 <param name="geneSource" value="indexed" />
                 <conditional name="GTFconditional">
                     <param name="GTFselect" value="without-gtf" />
-                    <param name="genomeDir" value="001" />
+                    <param name="genomeDir" value="000" />
                 </conditional>
             </conditional>
             <conditional name="twopass">
diff -r d82339e37e8e -r 41929aa1e7f3 test-data/rnastar_index2_versioned.loc
--- a/test-data/rnastar_index2_versioned.loc	Thu Aug 15 01:54:13 2019 -0400
+++ b/test-data/rnastar_index2_versioned.loc	Sat Aug 17 09:38:21 2019 -0400
@@ -1,4 +1,4 @@
 ##STAR versioned indexes
 #build_id	dbkey	display_name	path	with_gene_model	version
 000	?	test_index	${__HERE__}/test-cache/tophat-test	0	2.7.1a
-001	?	test_index2	${__HERE__}/test-cache/tophat-test	1	2.7.1a
+001	?	test_index_with_gene_model	${__HERE__}/test-cache/tophat-test	1	2.7.1a