# HG changeset patch
# User iuc
# Date 1466887479 14400
# Node ID ecbdfc775b9a56124e5d805ac048eec8de7b829e
# Parent  ae9382cfb6ac0cabbab01e30b95db17d3f048a32
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98

diff -r ae9382cfb6ac -r ecbdfc775b9a jbrowse.xml
--- a/jbrowse.xml	Sat Jun 25 15:06:43 2016 -0400
+++ b/jbrowse.xml	Sat Jun 25 16:44:39 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse" name="JBrowse" version="0.5">
+<tool id="jbrowse" name="JBrowse" version="0.5.2">
   <description>genome browser</description>
   <macros>
     <import>macros.xml</import>
@@ -72,11 +72,13 @@
     <metadata>
         <gencode>$gencode</gencode>
         <genomes>
-            #if str($action.genomes) != "None":
-            #for $genome in $action.genomes:
-                <genome>$genome</genome>
-            #end for
-            #end if
+              #if str($action.reference_genome.genome_type_select) == "indexed":
+                <genome>${action.reference_genome.genomes.fields.path}</genome>
+              #else
+                #for $genome in $action.reference_genome.genomes:
+                    <genome>$genome</genome>
+                #end for
+              #end if
         </genomes>
         <general>
             <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
@@ -224,20 +226,13 @@
             <option value="update">Update exising JBrowse Instance</option>
         </param>
         <when value="create">
-            <param label="Fasta Sequence(s)"
-                   name="genomes"
-                   type="data"
-                   format="fasta"
-                   multiple="True"/>
+            <expand macro="genome_selector" />
        </when>
         <when value="update">
-            <param label="Additional Fasta Sequence(s)"
-                   help="If sequences are selected, they will be added to the existing JBrowse instance. You should not select any sequences if you are simply updating an existing JBrowse instance which already has the required reference sequences."
-                   name="genomes"
-                   type="data"
-                   format="fasta"
-                   optional="True"
-                   multiple="True"/>
+            <expand macro="genome_selector"
+              label="Additional Fasta Sequence(s)"
+              help="If sequences are selected, they will be added to the existing JBrowse instance. You should not select any sequences if you are simply updating an existing JBrowse instance which already has the required reference sequences."
+              optional="True"/>
             <param label="Previous JBrowse Instance"
                    name="update_jbrowse"
                    type="data"
diff -r ae9382cfb6ac -r ecbdfc775b9a macros.xml
--- a/macros.xml	Sat Jun 25 15:06:43 2016 -0400
+++ b/macros.xml	Sat Jun 25 16:44:39 2016 -0400
@@ -28,6 +28,43 @@
 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
 ]]>
   </token>
+  
+  <xml name="genome_selector"
+    token_help=""
+    token_label="Fasta sequences"
+    token_optional="False" >
+    <conditional name="reference_genome">
+        <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
+            <option selected="True" value="indexed">Use a built-in genome</option>
+            <option value="history">Use a genome from history</option>
+        </param>
+        <when value="indexed">
+            <param 
+              help="@HELP@"
+              label="@LABEL@"
+              name="genomes"
+              type="select"
+              optional="@OPTIONAL@"
+              >
+                <options from_data_table="all_fasta">
+                    <filter column="2" type="sort_by" />
+                    <validator message="No genomes are available for the selected input dataset" type="no_options" />
+                </options>
+            </param>
+        </when>
+        <when value="history">
+            <param 
+              format="fasta"
+              label="@LABEL@"
+              help="@HELP@"
+              name="genomes"
+              type="data"
+              optional="@OPTIONAL@"
+              multiple="True" />
+        </when>
+    </conditional>
+  </xml>
+  
   <xml name="auto_manual_tk"
       token_cond_label="Color"
       token_cond_name="color"
@@ -220,8 +257,8 @@
   </xml>
   <xml name="track_styling"
        token_classname="feature"
-       token_label="name,id"
-       token_description="note,description"
+       token_label="prodcut,name,id"
+       token_description="note"
        token_height="100px">
     <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
         <param label="JBrowse style.className" type="text"