# HG changeset patch
# User iuc
# Date 1510843485 18000
# Node ID 836d1aa3e89a057e2dbbe1d0be59528a2b7c02cf
# Parent  ff11d442feedce38938c803f83f92a24c8a641a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e

diff -r ff11d442feed -r 836d1aa3e89a jbrowse.xml
--- a/jbrowse.xml	Wed Nov 15 15:15:27 2017 -0500
+++ b/jbrowse.xml	Thu Nov 16 09:44:45 2017 -0500
@@ -1,11 +1,11 @@
-<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.2">
+<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.3">
   <description>genome browser</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <version_command>python jbrowse.py --version</version_command>
+  <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
   <command><![CDATA[
 
 #if $action.action_select == "create":
@@ -19,7 +19,7 @@
 cp $trackxml $output.files_path/galaxy.xml &&
 
 ## Once that's done, we run the python script to handle the real work
-python $__tool_directory__/jbrowse.py
+python '$__tool_directory__/jbrowse.py'
 
 --jbrowse \${JBROWSE_SOURCE_DIR}
 #if str($standalone) == "Complete":
@@ -73,7 +73,9 @@
         <gencode>$gencode</gencode>
         <genomes>
             #if str($reference_genome.genome_type_select) == "indexed":
-              <genome>${reference_genome.genomes.fields.path}</genome>
+              <genome path="${reference_genome.genomes.fields.path}">
+                  <metadata />
+              </genome>s
             #else
               #for $genome in $reference_genome.genomes:
                   <genome path="$genome">
@@ -495,7 +497,8 @@
                                   help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
                                   optional="True"/>
                       </section>
-                   </when>
+                  </when>
+                  <when value="BlastView/View/Track/CanvasFeatures" />
                 </conditional>
                 <expand macro="track_styling" />
                 <expand macro="color_selection" />
@@ -904,6 +907,15 @@
         <param name="uglyTestingHack" value="enabled" />
         <output name="output" file="track_config/test.xml" lines_diff="26"/>
     </test>
+    <test>
+        <!-- data_table -->
+        <param name="reference_genome|genome_type_select" value="indexed"/>
+        <param name="reference_genome|genomes" value="merlin"/>
+        <param name="gencode" value="1" />
+        <param name="standalone" value="Data Directory" />
+        <param name="uglyTestingHack" value="enabled" />
+        <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
+    </test>
   </tests>
   <help><![CDATA[
 JBrowse-in-Galaxy
diff -r ff11d442feed -r 836d1aa3e89a readme.rst
--- a/readme.rst	Wed Nov 15 15:15:27 2017 -0500
+++ b/readme.rst	Thu Nov 16 09:44:45 2017 -0500
@@ -7,7 +7,7 @@
 Thus, it makes an ideal fit with Galaxy, especially for use as a
 workflow summary. E.g. annotate a genome, then visualise all of the
 associated datasets as an interactive HTML page. This tool MUST be whitelisted
-(or ``sanitize_all_html=False``) to function correctly.
+(or ``sanitize_all_html=False`` in galaxy.ini) to function correctly.
 
 Installation
 ============
@@ -17,7 +17,7 @@
 Running Locally
 ===============
 
-The Galaxy tool interface writes out a yaml file which is then used to generate
+The Galaxy tool interface writes out a xml file which is then used to generate
 the visualizations. An example used during development/testing can be seen in
 `test-data/*/test.xml`. The format is in no way rigorously defined and is
 likely to change at any time! Beware. ;)
@@ -25,6 +25,8 @@
 History
 =======
 
+-  0.7 Support for plugins (currently GC Content, Bookmarks, ComboTrackSelector),
+   track metadata
 -  0.5.2 Support for CanvasFeatures options.
 -  0.5.1 Support for contextual menus. Conda tests.
 -  0.5 Update existing instances on disk. Index names. Support HTML tracks
diff -r ff11d442feed -r 836d1aa3e89a test-data/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Thu Nov 16 09:44:45 2017 -0500
@@ -0,0 +1,19 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
+merlin	merlin	Merlin	${__HERE__}/merlin.fa
diff -r ff11d442feed -r 836d1aa3e89a test-data/gencode/test-data_table.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gencode/test-data_table.xml	Thu Nov 16 09:44:45 2017 -0500
@@ -0,0 +1,32 @@
+<?xml version="1.0"?>
+<root>
+    <metadata>
+        <gencode>1</gencode>
+        <genomes>
+              <genome path="/home/abretaud/iuc_tools_abretaud/tools/jbrowse/test-data/merlin.fa">
+                  <metadata />
+              </genome>s
+        </genomes>
+        <general>
+            <defaultLocation></defaultLocation>
+            <trackPadding>20</trackPadding>
+
+            <shareLink>true</shareLink>
+            <aboutDescription></aboutDescription>
+            <show_tracklist>true</show_tracklist>
+            <show_nav>true</show_nav>
+            <show_overview>true</show_overview>
+            <show_menu>true</show_menu>
+            <hideGenomeOptions>false</hideGenomeOptions>
+        </general>
+        <galaxyUrl>http://localhost:8080</galaxyUrl>
+    </metadata>
+    <tracks>
+    </tracks>
+    <plugins
+        ComboTrackSelector=""
+        Bookmarks=""
+        GCContent=""
+        theme=""
+        />
+</root>
diff -r ff11d442feed -r 836d1aa3e89a tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Thu Nov 16 09:44:45 2017 -0500
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+</tables>