Mercurial > repos > david-hoover > garbage1
diff variant_combine.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/variant_combine.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/variant_combine.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_combine" name="Combine Variants" version="0.0.2"> +<tool id="gatk2_variant_combine" name="Combine Variants" version="0.0.3"> <description></description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -15,11 +15,11 @@ #silent $priority_order.append( $input_variant_name ) #end for -p 'java - -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar" + -jar "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/GenomeAnalysisTK.jar" -T "CombineVariants" --out "${output_variants}" ##--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 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" @@ -407,11 +407,11 @@ Combines VCF records from different sources; supports both full merges and set unions. Merge: combines multiple records into a single one; if sample names overlap then they are uniquified. Union: assumes each rod represents the same set of samples (although this is not enforced); using the priority list (if provided), emits a single record instance at every position represented in the rods. -For more information on using the CombineVariants module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/CombineVariants>`_. +For more information on using the CombineVariants module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_CombineVariants.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>`_. ------ @@ -426,7 +426,7 @@ The output is a combined vcf file. -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. ------- @@ -449,7 +449,9 @@ 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>