changeset 41:8774b28235bb draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"

--- a/jbrowse-fromdir.xml	Fri Aug 21 04:42:41 2020 -0400
+++ b/jbrowse-fromdir.xml	Thu Dec 31 16:00:42 2020 +0000
@@ -3,6 +3,13 @@
   <macros>
     <import>macros.xml</import>
   </macros>
+  <edam_operations>
+    <edam_operation>operation_3434</edam_operation>
+  </edam_operations>
+  <edam_topics>
+    <edam_topic>topic_3307</edam_topic>
+    <edam_topic>topic_0092</edam_topic>
+  </edam_topics>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ## Create output directory

--- a/jbrowse.py	Fri Aug 21 04:42:41 2020 -0400
+++ b/jbrowse.py	Thu Dec 31 16:00:42 2020 +0000
@@ -400,6 +400,14 @@
     def _jbrowse_bin(self, command):
         return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
 
+    def symlink_or_copy(self, src, dest):
+        if 'GALAXY_JBROWSE_SYMLINKS' in os.environ and bool(os.environ['GALAXY_JBROWSE_SYMLINKS']):
+            cmd = ['ln', '-s', src, dest]
+        else:
+            cmd = ['cp', src, dest]
+
+        return self.subprocess_check_call(cmd)
+
     def process_genomes(self):
         for genome_node in self.genome_paths:
             # We only expect one input genome per run. This for loop is just
@@ -507,8 +515,7 @@
 
     def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
         dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
-        cmd = ['cp', data, dest]
-        self.subprocess_check_call(cmd)
+        self.symlink_or_copy(os.path.realpath(data), dest)
 
         url = os.path.join('raw', trackData['label'] + '.bw')
         trackData.update({
@@ -535,8 +542,7 @@
         urls = []
         for idx, bw in enumerate(data):
             dest = os.path.join('data', 'raw', trackData['label'] + '_' + str(idx) + '.bw')
-            cmd = ['ln', '-s', bw[1], dest]
-            self.subprocess_check_call(cmd)
+            self.symlink_or_copy(bw[1], dest)
 
             urls.append({"url": os.path.join('raw', trackData['label'] + '_' + str(idx) + '.bw'), "name": str(idx + 1) + ' - ' + bw[0]})
 
@@ -598,11 +604,8 @@
 
     def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
         dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
-        cmd = ['ln', '-s', os.path.realpath(data), dest]
-        self.subprocess_check_call(cmd)
-
-        cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai']
-        self.subprocess_check_call(cmd)
+        self.symlink_or_copy(os.path.realpath(data), dest)
+        self.symlink_or_copy(os.path.realpath(bam_index), dest + '.bai')
 
         url = os.path.join('raw', trackData['label'] + '.bam')
         trackData.update({

--- a/jbrowse.xml	Fri Aug 21 04:42:41 2020 -0400
+++ b/jbrowse.xml	Thu Dec 31 16:00:42 2020 +0000
@@ -3,7 +3,18 @@
   <macros>
     <import>macros.xml</import>
   </macros>
+  <xrefs>
+    <xref type="bio.tools">jbrowse</xref>
+  </xrefs>
   <expand macro="requirements"/>
+  <edam_operations>
+    <edam_operation>operation_0573</edam_operation>
+    <edam_operation>operation_0564</edam_operation>
+  </edam_operations>
+  <edam_topics>
+    <edam_topic>topic_3307</edam_topic>
+    <edam_topic>topic_0092</edam_topic>
+  </edam_topics>
   <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
   <command detect_errors="aggressive"><![CDATA[
 #if $action.action_select == "create":
@@ -667,7 +678,6 @@
   </outputs>
   <tests>
     <test>
-      <!-- gencode -->
       <param name="reference_genome|genome_type_select" value="history"/>
       <param name="reference_genome|genome" value="merlin.fa"/>
       <param name="gencode" value="1" />

--- a/macros.xml	Fri Aug 21 04:42:41 2020 -0400
+++ b/macros.xml	Thu Dec 31 16:00:42 2020 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-  <token name="@TOOL_VERSION@">1.16.9</token>
+  <token name="@TOOL_VERSION@">1.16.10</token>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">jbrowse</requirement>

--- a/readme.rst	Fri Aug 21 04:42:41 2020 -0400
+++ b/readme.rst	Thu Dec 31 16:00:42 2020 +0000
@@ -25,6 +25,15 @@
 History
 =======
 
+- 1.16.10+galaxy0
+
+    - UPDATED to JBrowse 1.16.10
+    - ADDED GALAXY_JBROWSE_SYMLINKS environment variable: if set, the tool will make symlinks to bam/bigwig files instead of copying them
+
+- 1.16.9+galaxy0
+
+    - UPDATED to JBrowse 1.16.9
+
 - 1.16.8+galaxy0
 
     - UPDATED to JBrowse 1.16.8