Mercurial > repos > david-hoover > garbage1
changeset 32:29507d31c174 draft
Uploaded
| author | david-hoover |
|---|---|
| date | Thu, 20 Sep 2012 12:03:32 -0400 |
| parents | 1326b011a3b9 |
| children | 642c7f54431a |
| files | base_recalibrator.xml depth_of_coverage.xml indel_realigner.xml print_reads.xml realigner_target_creator.xml unified_genotyper.xml variant_annotator.xml variant_apply_recalibration.xml variant_combine.xml variant_eval.xml variant_filtration.xml variant_recalibrator.xml variant_select.xml variants_validate.xml |
| diffstat | 14 files changed, 138 insertions(+), 113 deletions(-) [+] |
line wrap: on
line diff
--- a/base_recalibrator.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/base_recalibrator.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_base_recalibrator" name="Base Recalibrator" version="0.0.2"> +<tool id="gatk2_base_recalibrator" name="Base Recalibrator" version="0.0.3"> <description>on BAM files</description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -12,10 +12,10 @@ -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index #end if -p 'java - -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar" + -jar "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/GenomeAnalysisTK.jar" -T "BaseRecalibrator" --num_threads 4 ##hard coded, for now - -et "NO_ET" -K "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/gatk2_key_file" ##ET no phone home + -et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home ##-log "${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}" @@ -560,7 +560,6 @@ solid_nocall_strategy Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ) recal_file Filename for the input covariates table recalibration .csv file out The output CSV file - recal_file Filename for the outputted covariates table recalibration file standard_covs Use the standard set of covariates in addition to the ones listed using the -cov argument run_without_dbsnp_potentially_ruining_quality If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only. @@ -570,6 +569,8 @@ 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>`_ +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>
--- 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>
--- a/indel_realigner.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/indel_realigner.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_indel_realigner" name="Indel Realigner" version="0.0.2"> +<tool id="gatk2_indel_realigner" name="Indel Realigner" version="0.0.3"> <description>- perform local realignment</description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -12,10 +12,10 @@ -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index #end if -p 'java - -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar" + -jar "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/GenomeAnalysisTK.jar" -T "IndelRealigner" -o "${output_bam}" - -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 ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": @@ -440,11 +440,11 @@ Performs local realignment of reads based on misalignments due to the presence of indels. Unlike most mappers, this walker uses the full alignment context to determine whether an appropriate alternate reference (i.e. indel) exists and updates SAMRecords accordingly. -For more information on local realignment around indels using the GATK, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels>`_. +For more information on local realignment around indels using the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_IndelRealigner.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>`_. ------ @@ -458,7 +458,7 @@ The output is in the BAM format. -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. ------- @@ -486,7 +486,9 @@ 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>
--- a/print_reads.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/print_reads.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_print_reads" name="Print Reads" version="0.0.2"> +<tool id="gatk2_print_reads" name="Print Reads" version="0.0.3"> <description>on BAM files</description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -12,11 +12,11 @@ -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index #end if -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 "PrintReads" -o "${output_bam}" - -et "NO_ET" -K "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/gatk2_key_file" ##ET no phone home - --num_threads 4 ##hard coded, for now + -et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home + ##--num_threads 4 ##not supported yet ##-log "${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}" @@ -461,17 +461,17 @@ This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads. Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with CovariateCounterWalker. -For more information on base quality score recalibration using the GATK, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration>`_. +For more information on base quality score recalibration using the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_PrintReads.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>`_. ------ **Inputs** -GenomeAnalysisTK: TableRecalibration accepts an aligned BAM and a recalibration CSV input files. +GenomeAnalysisTK: PrintReads accepts an aligned BAM and a recalibration CSV input files. **Outputs** @@ -479,7 +479,7 @@ The output is in BAM format. -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. ------- @@ -510,7 +510,9 @@ 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>
--- a/realigner_target_creator.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/realigner_target_creator.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="0.0.2"> +<tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="0.0.3"> <description>for use in local realignment</description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -12,10 +12,10 @@ -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index #end if -p 'java - -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar" + -jar "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/GenomeAnalysisTK.jar" -T "RealignerTargetCreator" -o "${output_interval}" - -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 --num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": @@ -408,11 +408,11 @@ Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string. -For more information on local realignment around indels using the GATK, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels>`_. +For more information on local realignment around indels using the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_RealignerTargetCreator.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 in GATK Interval format. -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. ------- @@ -443,7 +443,9 @@ 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>
--- a/unified_genotyper.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/unified_genotyper.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="0.0.2"> +<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="0.0.3"> <description>SNP and indel caller</description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -14,12 +14,12 @@ #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 "UnifiedGenotyper" --num_threads 4 ##hard coded, for now --out "${output_vcf}" --metrics_file "${output_metrics}" - -et "NO_ET" -K "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/gatk2_key_file" ##ET no phone home + -et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home ##-log "${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}" @@ -552,11 +552,11 @@ A variant caller which unifies the approaches of several disparate callers. Works for single-sample and multi-sample data. The user can choose from several different incorporated calculation models. -For more information on the GATK Unified Genotyper, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Unified_genotyper>`_. +For more information on the GATK Unified Genotyper, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.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>`_. ------ @@ -570,7 +570,7 @@ The output is in VCF format. -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. ------- @@ -605,7 +605,9 @@ 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>
--- a/variant_annotator.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/variant_annotator.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_annotator" name="Variant Annotator" version="0.0.2"> +<tool id="gatk2_variant_annotator" name="Variant Annotator" version="0.0.3"> <description></description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -15,11 +15,11 @@ #end if -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" -p 'java - -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar" + -jar "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/GenomeAnalysisTK.jar" ##--list -T "VariantAnnotator" ##--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}" @@ -496,11 +496,11 @@ Annotates variant calls with context information. Users can specify which of the available annotations to use. -For more information on using the VariantAnnotator, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator>`_. +For more information on using the VariantAnnotator, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.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>`_. ------ @@ -515,7 +515,7 @@ The output is in VCF format. -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. ------- @@ -534,7 +534,9 @@ 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>
--- a/variant_apply_recalibration.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/variant_apply_recalibration.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.2"> +<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.3"> <description></description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -10,10 +10,10 @@ -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" #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 "ApplyRecalibration" ##--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 @@ -370,11 +370,11 @@ Applies cuts to the input vcf file (by adding filter lines) to achieve the desired novel FDR levels which were specified during VariantRecalibration -For more information on using the ApplyRecalibration module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration>`_. +For more information on using the ApplyRecalibration module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_ApplyRecalibration.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>`_. ------ @@ -387,8 +387,7 @@ The output is in VCF format. - -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. ------- @@ -408,7 +407,9 @@ 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>
--- 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>
--- a/variant_eval.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/variant_eval.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_eval" name="Eval Variants" version="0.0.2"> +<tool id="gatk2_variant_eval" name="Eval Variants" version="0.0.3"> <description></description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -11,11 +11,11 @@ -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}" #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 "VariantEval" --out "${output_report}" --num_threads 4 ##hard coded, for now - -et "NO_ET" -K "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/gatk2_key_file" ##ET no phone home + -et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home ##-log "${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}" @@ -518,11 +518,11 @@ General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more) -For more information on using the VariantEval module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/VariantEval>`_. +For more information on using the VariantEval module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_varianteval_VariantEval.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>`_. ------ @@ -536,8 +536,7 @@ The output is a table of variant evaluation. -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. ------- @@ -566,7 +565,9 @@ 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>
--- a/variant_filtration.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/variant_filtration.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_filtration" name="Variant Filtration" version="0.0.2"> +<tool id="gatk2_variant_filtration" name="Variant Filtration" version="0.0.3"> <description>on VCF files</description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -9,10 +9,10 @@ --stdout "${output_log}" -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" -p 'java - -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar" + -jar "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/GenomeAnalysisTK.jar" -T "VariantFiltration" ##--num_threads 4 ##hard coded, for now - -et "NO_ET" -K "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/gatk2_key_file" ##ET no phone home + -et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home -o "${output_vcf}" ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": @@ -411,11 +411,11 @@ Filters variant calls using a number of user-selectable, parameterizable criteria. -For more information on using the VariantFiltration module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/VariantFiltrationWalker>`_. +For more information on using the VariantFiltration module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_filters_VariantFiltration.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>`_. ------ @@ -428,8 +428,7 @@ The output is in VCF format. - -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. ------- @@ -451,7 +450,10 @@ 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>
--- a/variant_recalibrator.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/variant_recalibrator.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="0.0.2"> +<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="0.0.3"> <description></description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -10,10 +10,10 @@ -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" #end for -p 'java - -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar" + -jar "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/GenomeAnalysisTK.jar" -T "VariantRecalibrator" --num_threads 4 ##hard coded, for now - -et "NO_ET" -K "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/gatk2_key_file"##ET no phone home + -et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file"##ET no phone home ##-log "${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}" @@ -656,11 +656,11 @@ Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score -For more information on using the VariantRecalibrator module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration>`_. +For more information on using the VariantRecalibrator module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_VariantRecalibrator.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>`_. ------ @@ -674,7 +674,7 @@ The output is in VCF format. -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. ------- @@ -709,7 +709,9 @@ 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>
--- a/variant_select.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/variant_select.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_select" name="Select Variants" version="0.0.2"> +<tool id="gatk2_variant_select" name="Select Variants" version="0.0.3"> <description>from VCF files</description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -9,10 +9,10 @@ --stdout "${output_log}" -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" -p 'java - -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar" + -jar "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/GenomeAnalysisTK.jar" -T "SelectVariants" --num_threads 4 ##hard coded, for now - -et "NO_ET" -K "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/gatk2_key_file" ##ET no phone home + -et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home -o "${output_vcf}" #if $reference_source.reference_source_selector != "history": @@ -515,11 +515,11 @@ Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP > 1000" (depth of coverage greater than 1000x), "AF < 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the Using JEXL expressions section (http://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions). One can optionally include concordance or discordance tracks for use in selecting overlapping variants. -For more information on using the SelectVariants module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/SelectVariants>`_. +For more information on using the SelectVariants module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.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>`_. ------ @@ -533,7 +533,7 @@ The output is in VCF format. -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. ------- @@ -568,7 +568,9 @@ 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>
--- a/variants_validate.xml Thu Sep 20 10:42:32 2012 -0400 +++ b/variants_validate.xml Thu Sep 20 12:03:32 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_validate_variants" name="Validate Variants" version="0.0.2"> +<tool id="gatk2_validate_variants" name="Validate Variants" version="0.0.3"> <description></description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -8,10 +8,10 @@ --stdout "${output_log}" -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" -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 "ValidateVariants" - -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 ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": @@ -359,11 +359,11 @@ Validates a variants file. -For more information on using the ValidateVariants module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/VariantValidator>`_. +For more information on using the ValidateVariants module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_ValidateVariants.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>`_. ------ @@ -377,7 +377,7 @@ The output is a log of variant validation. -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. ------- @@ -392,7 +392,9 @@ 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>