Mercurial > repos > iuc > gemini_actionable_mutations
changeset 4:4a1e53517dba draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
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--- a/gemini_actionable_mutations.xml Fri Dec 14 12:34:23 2018 -0500 +++ b/gemini_actionable_mutations.xml Mon Dec 17 12:11:45 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> +<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@"> <description>Retrieve genes with actionable somatic mutations via COSMIC and DGIdb</description> <macros> <import>gemini_macros.xml</import>
--- a/gemini_macros.xml Fri Dec 14 12:34:23 2018 -0500 +++ b/gemini_macros.xml Mon Dec 17 12:11:45 2018 -0500 @@ -1,15 +1,12 @@ <macros> <!-- gemini version to be used --> - <token name="@VERSION@">0.18.1</token> + <token name="@VERSION@">0.20.1</token> <!-- minimal annotation files version required by this version of gemini --> - <token name="@DB_VERSION@">181</token> + <token name="@DB_VERSION@">200</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">gemini</requirement> - <requirement type="package" version="0.2.6">tabix</requirement> - <!-- for conda useage --> - <!--requirement type="package" version="1.3.1">htslib</requirement--> <yield /> </requirements> </xml>
--- a/test-data/gemini_versioned_databases.loc Fri Dec 14 12:34:23 2018 -0500 +++ b/test-data/gemini_versioned_databases.loc Mon Dec 17 12:11:45 2018 -0500 @@ -1,3 +1,3 @@ ## GEMINI versioned databases #DownloadDate dbkey DBversion Description Path -1999-01-01 hg19 181 GEMINI annotations (test snapshot) ${__HERE__}/test-cache +1999-01-01 hg19 200 GEMINI annotations (test snapshot) ${__HERE__}/test-cache
--- a/test-data/test-cache/gemini-config.yaml Fri Dec 14 12:34:23 2018 -0500 +++ b/test-data/test-cache/gemini-config.yaml Mon Dec 17 12:11:45 2018 -0500 @@ -2,12 +2,14 @@ versions: ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz: 4 ESP6500SI.all.snps_indels.tidy.v2.vcf.gz: 2 - ExAC.r0.3.sites.vep.tidy.vcf.gz: 3 + ExAC.r0.3.sites.vep.tidy.vcf.gz: 4 GRCh37-gms-mappability.vcf.gz: 2 - clinvar_20160203.tidy.vcf.gz: 5 + clinvar_20170130.tidy.vcf.gz: 5 cosmic-v68-GRCh37.tidy.vcf.gz: 3 - dbsnp.b141.20140813.hg19.tidy.vcf.gz: 4 + dbsnp.b147.20160601.tidy.vcf.gz: 1 detailed_gene_table_v75: 2 geno2mp.variants.tidy.vcf.gz: 1 + gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz: 2 hg19.rmsk.bed.gz: 2 summary_gene_table_v75: 2 + whole_genome_SNVs.tsv.compressed.gz: 2