Mercurial > repos > david-hoover > garbage1
diff depth_of_coverage.xml @ 32:29507d31c174 draft
Uploaded
| author | david-hoover |
|---|---|
| date | Thu, 20 Sep 2012 12:03:32 -0400 |
| parents | 1326b011a3b9 |
| children | 642c7f54431a |
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--- a/depth_of_coverage.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/depth_of_coverage.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.2"> +<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.3"> <description>on BAM files</description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -14,11 +14,11 @@ #end if #end for -p 'java - -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar" + -jar "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/GenomeAnalysisTK.jar" -T "DepthOfCoverage" ##--num_threads 4 ##hard coded, for now - -et "NO_ET" -K "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/gatk2_key_file" ##ET no phone home + -et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" #end if @@ -971,11 +971,11 @@ DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score. -For more information on the GATK Depth of Coverage, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Depth_of_Coverage>`_. +For more information on the GATK Depth of Coverage, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthOfCoverage.html>`_. -To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_. +To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. -If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_. +If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. ------ @@ -989,7 +989,7 @@ The output is in various table formats. -Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats. +Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. ------- @@ -1021,7 +1021,9 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* +Please also site `McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303. Epub 2010 Jul 19. <http://www.ncbi.nlm.nih.gov/pubmed/20644199>`_ + +If you use this tool in Galaxy, please cite `Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. <http://www.ncbi.nlm.nih.gov/pubmed/20069535>`_ </help> </tool>