Mercurial > repos > iuc > jbrowse
changeset 22:5f70e7fe6077 draft
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(-) [+] |
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--- 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"/>