Mercurial > repos > iuc > jbrowse

changeset 22:5f70e7fe6077 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author iuc
date Tue, 30 Oct 2018 18:57:53 -0400
parents 1c718d8b3532
children dba3c47e1798
files jbrowse-fromdir.xml jbrowse.py jbrowse.xml
diffstat 3 files changed, 8 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/jbrowse-fromdir.xml	Tue Sep 11 07:11:44 2018 -0400
+++ b/jbrowse-fromdir.xml	Tue Oct 30 18:57:53 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="@WRAPPER_VERSION@">
+<tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
   <description>upgrades the bare data directory to a full JBrowse instance</description>
   <macros>
     <import>macros.xml</import>
--- a/jbrowse.py	Tue Sep 11 07:11:44 2018 -0400
+++ b/jbrowse.py	Tue Oct 30 18:57:53 2018 -0400
@@ -31,7 +31,7 @@
     }}
     """
 
-    COLOR_FUNCTION_TEMPLATE_QUAL = """
+    COLOR_FUNCTION_TEMPLATE_QUAL = r"""
     function(feature, variableName, glyphObject, track) {{
         var search_up = function self(sf, attr){{
             if(sf.get(attr) !== undefined){{
--- a/jbrowse.xml	Tue Sep 11 07:11:44 2018 -0400
+++ b/jbrowse.xml	Tue Oct 30 18:57:53 2018 -0400
@@ -7,7 +7,6 @@
   <expand macro="stdio"/>
   <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
   <command><![CDATA[
-
 #if $action.action_select == "create":
     mkdir -p $output.files_path &&
 #else:
@@ -35,15 +34,13 @@
     mv $dummyIndex $output;
 #end if
 
-
 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
 #if str($uglyTestingHack) == "enabled":
     mv $trackxml $output
 #end if
-]]></command>
+  ]]></command>
   <configfiles>
-      <configfile name="dummyIndex">
-      <![CDATA[
+      <configfile name="dummyIndex"><![CDATA[
       <html>
           <head>
           </head>
@@ -65,8 +62,7 @@
               </p>
           </body>
       </html>
-          ]]>
-      </configfile>
+      ]]></configfile>
       <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
 <root>
     <metadata>
@@ -345,9 +341,9 @@
         </when>
     </conditional>
 
-    <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/>
+    <param name="standalone" type="boolean" truevalue="Complete" falsevalue="Data Directory" checked="true" label="Produce Standalone Instance" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo"/>
 
-    <param label="Genetic Code" name="gencode" type="select">
+    <param name="gencode" type="select" label="Genetic Code">
       <option value="1">1. The Standard Code</option>
       <option value="2">2. The Vertebrate Mitochondrial Code</option>
       <option value="3">3. The Yeast Mitochondrial Code</option>
@@ -375,10 +371,7 @@
         </param>
         <when value="create" />
         <when value="update">
-            <param label="Previous JBrowse Instance"
-                   name="update_jbrowse"
-                   type="data"
-                   format="html" />
+            <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" />
         </when>
     </conditional>
 
@@ -1191,7 +1184,6 @@
    scores. Manually specify minimum and maximum score attributes, or do
    not use varied colours based on scores to avoid this issue.
 
-
 @ATTRIBUTION@
 ]]></help>
   <expand macro="citations"/>