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Update help for some SAMTools.

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Daniel Blankenberg
2011-11-21 16:55:16 -05:00
parent d5f735faac
commit c1dd3d3eaa
5 changed files with 34 additions and 0 deletions
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tools/samtools/bam_to_sam.xml
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@@ -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>`_
</help>
</tool>
tools/samtools/sam_pileup.xml
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@@ -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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
</help>
</tool>
tools/samtools/sam_to_bam.xml
+6
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@@ -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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
</help>
</tool>
tools/samtools/samtools_flagstat.xml
+8
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@@ -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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
</help>
</tool>
tools/samtools/samtools_rmdup.xml
+8
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@@ -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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
</help>
</tool>