diff variant_annotator.xml @ 32:29507d31c174 draft

Uploaded

--- 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 &lt;http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator&gt;`_.
+For more information on using the VariantAnnotator, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.html&gt;`_.
 
-To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3&gt;`_.
+To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
 
-If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.
+If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
 
 ------
 
@@ -515,7 +515,7 @@
 The output is in VCF format.
 
 
-Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.
+Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21478889&gt;`_
 
-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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20644199&gt;`_
+
+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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20069535&gt;`_
 
   </help>
 </tool>