diff --git a/tools/samtools/bam_to_sam.xml b/tools/samtools/bam_to_sam.xml index 2a72324e481..e9ea217c3f7 100644 --- a/tools/samtools/bam_to_sam.xml +++ b/tools/samtools/bam_to_sam.xml @@ -56,5 +56,11 @@ This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + diff --git a/tools/samtools/sam_pileup.xml b/tools/samtools/sam_pileup.xml index 430582962bf..bdb3fe92822 100644 --- a/tools/samtools/sam_pileup.xml +++ b/tools/samtools/sam_pileup.xml @@ -177,6 +177,12 @@ where:: .. _consensus: http://samtools.sourceforge.net/cns0.shtml +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + diff --git a/tools/samtools/sam_to_bam.xml b/tools/samtools/sam_to_bam.xml index 9b295cfb2e0..7364bb4fdac 100644 --- a/tools/samtools/sam_to_bam.xml +++ b/tools/samtools/sam_to_bam.xml @@ -87,5 +87,11 @@ This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a s .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + diff --git a/tools/samtools/samtools_flagstat.xml b/tools/samtools/samtools_flagstat.xml index 5ccc412d47c..eae54b768ec 100644 --- a/tools/samtools/samtools_flagstat.xml +++ b/tools/samtools/samtools_flagstat.xml @@ -25,5 +25,13 @@ This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + diff --git a/tools/samtools/samtools_rmdup.xml b/tools/samtools/samtools_rmdup.xml index b9b7424bdec..835310c8422 100644 --- a/tools/samtools/samtools_rmdup.xml +++ b/tools/samtools/samtools_rmdup.xml @@ -57,5 +57,13 @@ This tool uses the SAMTools_ toolkit to remove potential PCR duplicates: if mult .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* +