From 2e7fdf2bffc8ca6e3673ae8ac27586b021ce0d46 Mon Sep 17 00:00:00 2001 From: Anton Nekrutenko Date: Fri, 25 Sep 2009 13:58:15 -0400 Subject: [PATCH] Added Cite to masthead --- templates/base_panels.mako | 11 ++++++++--- tools/fastx_toolkit/fastq_to_fasta.xml | 2 +- tools/samtools/pileup_parser.xml | 4 ++-- tools/samtools/sam_pileup.xml | 4 ++-- universe_wsgi.ini.sample | 2 ++ 5 files changed, 15 insertions(+), 8 deletions(-) diff --git a/templates/base_panels.mako b/templates/base_panels.mako index f303a1197e9..fa3dc5db66f 100644 --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -167,12 +167,17 @@
+ + Cite + + + User <% @@ -282,7 +287,7 @@ -
+
## Background displays first
## Layer iframes over backgrounds diff --git a/tools/fastx_toolkit/fastq_to_fasta.xml b/tools/fastx_toolkit/fastq_to_fasta.xml index fcde683f6df..fe4496f0ed9 100644 --- a/tools/fastx_toolkit/fastq_to_fasta.xml +++ b/tools/fastx_toolkit/fastq_to_fasta.xml @@ -3,7 +3,7 @@ gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v - + diff --git a/tools/samtools/pileup_parser.xml b/tools/samtools/pileup_parser.xml index 29dee0f46ae..571d3750a0e 100644 --- a/tools/samtools/pileup_parser.xml +++ b/tools/samtools/pileup_parser.xml @@ -1,5 +1,5 @@ - - to find variants + + on coverage and SNPs #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" $out_file1 diff --git a/tools/samtools/sam_pileup.xml b/tools/samtools/sam_pileup.xml index e4bd9ed2101..e2084dafc0e 100644 --- a/tools/samtools/sam_pileup.xml +++ b/tools/samtools/sam_pileup.xml @@ -1,5 +1,5 @@ - - generates the pileup format for a provided BAM file + + from BAM dataset sam_pileup.py --input1=$input1 diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample index 6b6b48f405f..97bee1de93e 100644 --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -102,9 +102,11 @@ static_style_dir = %(here)s/static/june_2007_style/blue ## 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 ------------------------------------------------