diff variant_select.xml @ 32:29507d31c174 draft

Uploaded

--- 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 &gt; 1000" (depth of coverage greater than 1000x), "AF &lt; 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 &lt;http://www.broadinstitute.org/gsa/wiki/index.php/SelectVariants&gt;`_.
+For more information on using the SelectVariants module, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.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;`_.
 
 ------
 
@@ -533,7 +533,7 @@
 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.
 
 -------
 
@@ -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. &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>