details: http://www.bx.psu.edu/hg/galaxy/rev/e5d57c9e2824 changeset: 2782:e5d57c9e2824 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Fri Sep 25 16:49:30 2009 -0400 description: Fixed an error in the help section of the Sam Pileup tool config 1 file(s) affected in this change: tools/samtools/sam_pileup.xml diffs (33 lines): diff -r dd50d8d45177 -r e5d57c9e2824 tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml Fri Sep 25 14:50:34 2009 -0400 +++ b/tools/samtools/sam_pileup.xml Fri Sep 25 16:49:30 2009 -0400 @@ -85,9 +85,9 @@ **Types of pileup datasets** -The description of pileup format below is largely based on information that can be found on SAMTools_ documentation page. The 6- and 10-column variants are described below. +The description of pileup format below is largely based on information that can be found on SAMTools Pileup_ documentation page. The 6- and 10-column variants are described below. -.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml +.. _Pileup: http://samtools.sourceforge.net/pileup.shtml **Six column pileup**:: @@ -111,7 +111,7 @@ **Ten column pileup** -The `ten-column`__ pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command:: +The `ten-column` (consensus_) pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command:: 1 2 3 4 5 6 7 8 9 10 @@ -137,7 +137,7 @@ 10 Quality values (phred33 scale, see Galaxy wiki for more) -.. __: http://samtools.sourceforge.net/cns0.shtml +.. _consensus: http://samtools.sourceforge.net/cns0.shtml </help>