| Previous changeset 3:26ad8a52d9fd (2016-06-25) Next changeset 5:12aa3ad29980 (2017-02-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f |
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modified:
macros.xml stacks_refmap.xml |
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added:
test-data/populations/batch_1.vcf |
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removed:
tool_dependencies.xml |
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| diff -r 26ad8a52d9fd -r 827c8c6ec4c1 macros.xml --- a/macros.xml Sat Jun 25 17:29:09 2016 -0400 +++ b/macros.xml Mon Sep 26 11:45:14 2016 -0400 |
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| @@ -2,14 +2,14 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.40">stacks</requirement> + <requirement type="package" version="1.42">stacks</requirement> <requirement type="package" version="1.2.10">velvet</requirement> - <container type="docker">quay.io/mulled/stacks:1.40--1</container> + <container type="docker">quay.io/mulled/stacks:1.42--2</container> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">1.40</token> + <token name="@WRAPPER_VERSION@">1.42</token> <xml name="stdio"> <stdio> @@ -86,6 +86,10 @@ <option value="taqI">taqI</option> <option value="xbaI">xbaI</option> <option value="xhoI">xhoI</option> + <option value="csp6I">csp6I</option> + <option value="bsaHI">bsaHI</option> + <option value="hpaII">hpaII</option> + <option value="ncoI">ncoI</option> </xml> <xml name="cross_types"> |
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| diff -r 26ad8a52d9fd -r 827c8c6ec4c1 stacks_refmap.xml --- a/stacks_refmap.xml Sat Jun 25 17:29:09 2016 -0400 +++ b/stacks_refmap.xml Mon Sep 26 11:45:14 2016 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.1"> +<tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.0"> <description>the Stacks pipeline with a reference genome (ref_map.pl)</description> <macros> <import>macros.xml</import> |
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| diff -r 26ad8a52d9fd -r 827c8c6ec4c1 test-data/populations/batch_1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/batch_1.vcf Mon Sep 26 11:45:14 2016 -0400 |
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| @@ -0,0 +1,12 @@ +##fileformat=VCFv4.2 +##fileDate=20160926 +##source="Stacks v1.42" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> +##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele Depth"> +##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihood"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PopA_01 PopA_02 +un 35 1_33 A C . PASS NS=2;AF=0.500 GT:DP:AD:GL 0/1:18:9,9:.,19.78,. 0/1:10:6,4:.,13.18,. +un 90 1_88 A C . PASS NS=2;AF=0.500 GT:DP:AD:GL 0/1:18:9,9:.,19.78,. 0/1:10:4,6:.,13.18,. |
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| diff -r 26ad8a52d9fd -r 827c8c6ec4c1 tool_dependencies.xml --- a/tool_dependencies.xml Sat Jun 25 17:29:09 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="stacks" version="1.40"> - <repository changeset_revision="51d4ab2c4dcf" name="package_stacks_1_40" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="velvet" version="1.2.10"> - <repository changeset_revision="93d32326537b" name="package_velvet_1_2_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |