[hg] galaxy 2778: Added Cite to masthead - galaxy-dev

2 Oct 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/40f58d95a051
changeset: 2778:40f58d95a051
user:      Anton Nekrutenko anton@bx.psu.edu
date:      Fri Sep 25 13:58:15 2009 -0400
description:
Added Cite to masthead
5 file(s) affected in this change:
templates/base_panels.mako
tools/fastx_toolkit/fastq_to_fasta.xml
tools/samtools/pileup_parser.xml
tools/samtools/sam_pileup.xml
universe_wsgi.ini.sample
diffs (80 lines):
diff -r 6a86a558f405 -r 40f58d95a051 templates/base_panels.mako

--- a/templates/base_panels.mako	Fri Sep 25 11:32:47 2009 -0400
+++ b/templates/base_panels.mako	Fri Sep 25 13:58:15 2009 -0400
@@ -167,11 +167,16 @@
         <div class="submenu">
         <ul>            
             <li><a href="${app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu"  )}">Email comments, bug reports, or suggestions</a></li>
-            <li><a target="_blank" href="${app.config.get( "wiki_url", "http://g2.trac.bx.psu.edu/" )}">Galaxy Wiki</a></li>             
-            <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://g2.trac.bx.psu.edu/wiki/ScreenCasts" )}">Video tutorials (screencasts)</a></li>
+            <li><a target="_blank" href="${app.config.get( "wiki_url", "http://bitbucket.org/galaxy/galaxy-central/wiki" )}">Galaxy Wiki</a></li>             
+            <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://galaxycast.org" )}">Video tutorials (screencasts)</a></li>
         </ul>
         </div>
     </td>
+    
+    <td class="tab">
+        <a target="_blank" href="${app.config.get( "citation_url", "http://bitbucket.org/galaxy/galaxy-central/wiki/Citations" )}">Cite</a>
+    </td>
+
<td class="tab">
         <a>User</a>
@@ -282,7 +287,7 @@
     </head>
<body scroll="no" class="${self.body_class}">
-	<div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;">
+	<div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 960px;">
         ## Background displays first
         <div id="background"></div>
         ## Layer iframes over backgrounds
diff -r 6a86a558f405 -r 40f58d95a051 tools/fastx_toolkit/fastq_to_fasta.xml
--- a/tools/fastx_toolkit/fastq_to_fasta.xml	Fri Sep 25 11:32:47 2009 -0400
+++ b/tools/fastx_toolkit/fastq_to_fasta.xml	Fri Sep 25 13:58:15 2009 -0400
@@ -3,7 +3,7 @@
    <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v </command>
<inputs>
-		<param format="fastqsolexa" name="input" type="data" label="FASTQ Library to convert" />
+		<param format="fastqsolexa,fastqsanger" name="input" type="data" label="FASTQ Library to convert" />
<param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
    		<option value="">yes</option>
diff -r 6a86a558f405 -r 40f58d95a051 tools/samtools/pileup_parser.xml
--- a/tools/samtools/pileup_parser.xml	Fri Sep 25 11:32:47 2009 -0400
+++ b/tools/samtools/pileup_parser.xml	Fri Sep 25 13:58:15 2009 -0400
@@ -1,5 +1,5 @@
-<tool id="pileup_parser" name="Parse pileup">
-  <description>to find variants</description>
+<tool id="pileup_parser" name="Filter pileup">
+  <description>on coverage and SNPs</description>
   <command interpreter="perl">
     #if   $pileup_type.type_select == "six":    #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1
     #elif $pileup_type.type_select == "ten":    #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1
diff -r 6a86a558f405 -r 40f58d95a051 tools/samtools/sam_pileup.xml
--- a/tools/samtools/sam_pileup.xml	Fri Sep 25 11:32:47 2009 -0400
+++ b/tools/samtools/sam_pileup.xml	Fri Sep 25 13:58:15 2009 -0400
@@ -1,5 +1,5 @@
-<tool id="sam_pileup" name="SAM Pileup Format" version="1.0.0">
-  <description>generates the pileup format for a provided BAM file</description>
+<tool id="sam_pileup" name="Generate pileup" version="1.0.0">
+  <description>from BAM dataset</description>
   <command interpreter="python">
     sam_pileup.py 
        --input1=$input1
diff -r 6a86a558f405 -r 40f58d95a051 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample	Fri Sep 25 11:32:47 2009 -0400
+++ b/universe_wsgi.ini.sample	Fri Sep 25 13:58:15 2009 -0400
@@ -102,9 +102,11 @@
 ## Brand: appends "/[brand]" to the "Galaxy" text in the masthead
 ## wiki_url: replaces the default galaxy main wiki
 ## bugs_email: replaces the default galaxy bugs email list
+##citation_url: point to a URL listing citations
 #brand = Private local mirror
 #wiki_url = /path/to/my/local/wiki
 #bugs_email = mailto:galaxy-bugs@example.org
+#citation_url = /path/to/my/citations
# ---- Logging and Debugging ------------------------------------------------

    