1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/36d42578940a/
changeset: 36d42578940a
user: dannon
date: 2011-08-05 17:31:12
summary: Update Param unit test to account for the '#' to '__pd__' change from 5810:b68bbdc8dd14 that made it fail.
affected #: 1 file (5 bytes)
--- a/lib/galaxy/util/__init__.py Fri Aug 05 11:18:58 2011 -0400
+++ b/lib/galaxy/util/__init__.py Fri Aug 05 11:31:12 2011 -0400
@@ -199,7 +199,7 @@
>>> par.symbols # replaces unknown symbols with X
['alpha', '__lt____gt__', 'XrmXX!']
>>> par.flatten() # flattening to a list
- [('status', 'on'), ('symbols', 'alpha'), ('symbols', '__lt____gt__'), ('symbols', 'XrmXX!')]
+ [('status', 'on'), ('symbols', 'alpha'), ('symbols', '__lt____gt__'), ('symbols', 'XrmX__pd__!')]
"""
# is NEVER_SANITIZE required now that sanitizing for tool parameters can be controlled on a per parameter basis and occurs via InputValueWrappers?
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/9f9c2612d3c6/
changeset: 9f9c2612d3c6
user: greg
date: 2011-08-04 19:50:09
summary: A couple of tool shed template fixes.
affected #: 2 files (176 bytes)
--- a/templates/webapps/community/repository/manage_repository.mako Thu Aug 04 13:43:21 2011 -0400
+++ b/templates/webapps/community/repository/manage_repository.mako Thu Aug 04 13:50:09 2011 -0400
@@ -161,14 +161,14 @@
%if can_set_metadata:
<p/><div class="toolForm">
- <div class="toolFormTitle">Repository metadata</div>
+ <div class="toolFormTitle">Preview tools and inspect metadata</div><div class="toolFormBody">
%if metadata:
%if 'tools' in metadata:
<div class="form-row"><table width="100%"><tr bgcolor="#D8D8D8" width="100%">
- <td><label>Tools:</label></td>
+ <td><b>Tools</b><i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i></td></tr></table></div>
@@ -224,7 +224,7 @@
<div class="form-row"><table width="100%"><tr bgcolor="#D8D8D8" width="100%">
- <td><label>Workflows:</label></td>
+ <td><b>Workflows</b></td></tr></table></div>
@@ -311,7 +311,7 @@
%endif
<p/><div class="toolForm">
- <div class="toolFormTitle">Grant authority to upload or push changes</div>
+ <div class="toolFormTitle">Grant authority to make changes</div><div class="toolFormBody"><table class="grid"><tr>
@@ -335,7 +335,7 @@
<label>Username:</label>
${allow_push_select_field.get_html()}
<div class="toolParamHelp" style="clear: both;">
- Multi-select usernames to grant permission to push to this repository
+ Multi-select usernames to grant permission to make changes to this repository
</div><div style="clear: both"></div></div>
--- a/templates/webapps/community/repository/view_repository.mako Thu Aug 04 13:43:21 2011 -0400
+++ b/templates/webapps/community/repository/view_repository.mako Thu Aug 04 13:50:09 2011 -0400
@@ -153,13 +153,13 @@
%if metadata:
<p/><div class="toolForm">
- <div class="toolFormTitle">Repository metadata</div>
+ <div class="toolFormTitle">Preview tools and inspect metadata</div><div class="toolFormBody">
%if 'tools' in metadata:
<div class="form-row"><table width="100%"><tr bgcolor="#D8D8D8" width="100%">
- <td><label>Tools:</label></td>
+ <td><b>Tools</b><i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i></td></tr></table></div>
@@ -215,7 +215,7 @@
<div class="form-row"><table width="100%"><tr bgcolor="#D8D8D8" width="100%">
- <td><label>Workflows:</label></td>
+ <td><b>Workflows</b></td></tr></table></div>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2c0fb36140bd/
changeset: 2c0fb36140bd
user: greg
date: 2011-08-04 19:43:21
summary: Missed a link in previous commit.
affected #: 1 file (7 bytes)
--- a/templates/webapps/community/base_panels.mako Thu Aug 04 13:39:58 2011 -0400
+++ b/templates/webapps/community/base_panels.mako Thu Aug 04 13:43:21 2011 -0400
@@ -33,7 +33,7 @@
<a>Help</a><div class="submenu"><ul>
- <li><a target="_blank" href="${app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/" )}">Support</a></li>
+ <li><a target="_blank" href="${app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" )}">Support</a></li><li><a target="_blank" href="${app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" )}">Galaxy Wiki</a></li><li><a target="_blank" href="${app.config.get( "screencasts_url", "http://galaxycast.org" )}">Video tutorials (screencasts)</a></li><li><a target="_blank" href="${app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" )}">How to Cite Galaxy</a></li>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/6bc991a9a86e/
changeset: 6bc991a9a86e
user: dan
date: 2011-08-04 19:30:01
summary: Make setting read groups in BWA off by default.
affected #: 2 files (32 bytes)
--- a/tools/sr_mapping/bwa_color_wrapper.xml Thu Aug 04 11:01:22 2011 -0400
+++ b/tools/sr_mapping/bwa_color_wrapper.xml Thu Aug 04 13:30:01 2011 -0400
@@ -134,7 +134,7 @@
<conditional name="readGroup"><param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)"><option value="yes">Yes</option>
- <option value="no">No</option>
+ <option value="no" selected="True">No</option></param><when value="yes"><param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG
--- a/tools/sr_mapping/bwa_wrapper.xml Thu Aug 04 11:01:22 2011 -0400
+++ b/tools/sr_mapping/bwa_wrapper.xml Thu Aug 04 13:30:01 2011 -0400
@@ -127,7 +127,7 @@
<conditional name="readGroup"><param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)"><option value="yes">Yes</option>
- <option value="no">No</option>
+ <option value="no" selected="True">No</option></param><when value="yes"><param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.