| Previous changeset 4:b8ab4ef85a5b (2014-06-25) |
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Commit message:
Uploaded |
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modified:
tool_dependencies.xml vcfvcfintersect.xml |
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| diff -r b8ab4ef85a5b -r 89c1efc31618 tool_dependencies.xml --- a/tool_dependencies.xml Wed Jun 25 16:51:34 2014 -0400 +++ b/tool_dependencies.xml Mon Sep 15 14:54:08 2014 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="vcflib" version="86723982aa"> - <repository changeset_revision="a6826babf644" name="vcflib_86723982aa" owner="anton" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="vcflib" version="8a5602bf07"> + <repository changeset_revision="bffe0495cd92" name="package_vcflib_8a5602bf07" owner="anton" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |
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| diff -r b8ab4ef85a5b -r 89c1efc31618 vcfvcfintersect.xml --- a/vcfvcfintersect.xml Wed Jun 25 16:51:34 2014 -0400 +++ b/vcfvcfintersect.xml Mon Sep 15 14:54:08 2014 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="0.0.2"> <requirements> - <requirement type="package" version="86723982aa">vcflib</requirement> + <requirement type="package" version="8a5602bf07">vcflib</requirement> <!-- <requirement type="package" version="0.1.18">samtools</requirement> --> </requirements> <description>Intersect two VCF datasets</description> @@ -78,7 +78,7 @@ <param name="reference_source_selector" value="history" /> <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> - <param name="isect_union" value="Intersect" /> + <param name="isect_union" value="-i" /> <param name="invert" value="False" /> <param name="loci" value="False" /> <patam name="adv_options" value="False" /> @@ -90,7 +90,7 @@ <param name="reference_source_selector" value="history" /> <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> - <param name="isect_union" value="Union" /> + <param name="isect_union" value="-u" /> <param name="invert" value="False" /> <param name="loci" value="False" /> <patam name="adv_options" value="False" /> @@ -109,7 +109,6 @@ -i, --intersect-vcf FILE use this VCF for set intersection generation -u, --union-vcf FILE use this VCF for set union generation -w, --window-size N compare records up to this many bp away (default 30) - -r, --reference FILE FASTA reference file, required with -i and -u -l, --loci output whole loci when one alternate allele matches -m, --ref-match intersect on the basis of record REF string -t, --tag TAG attach TAG to each record's info field if it would intersect |