Mercurial > repos > iuc > gemini_actionable_mutations

changeset 4:4a1e53517dba draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
author iuc
date Mon, 17 Dec 2018 12:11:45 -0500
parents 5fb59611125e
children dfa34415e979
files gemini_actionable_mutations.xml gemini_macros.xml test-data/gemini_amend_input.db test-data/gemini_annotate_result.db test-data/gemini_auto_dom_input.db test-data/gemini_auto_rec_input.db test-data/gemini_comphets_input.db test-data/gemini_de_novo_input.db test-data/gemini_is_somatic_result.db test-data/gemini_load_result1.db test-data/gemini_load_result2.db test-data/gemini_versioned_databases.loc test-data/test-cache/gemini-config.yaml test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi
diffstat 23 files changed, 9 insertions(+), 10 deletions(-) [+]
line wrap: on
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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>
Binary file test-data/gemini_amend_input.db has changed
Binary file test-data/gemini_annotate_result.db has changed
Binary file test-data/gemini_auto_dom_input.db has changed
Binary file test-data/gemini_auto_rec_input.db has changed
Binary file test-data/gemini_comphets_input.db has changed
Binary file test-data/gemini_de_novo_input.db has changed
Binary file test-data/gemini_is_somatic_result.db has changed
Binary file test-data/gemini_load_result1.db has changed
Binary file test-data/gemini_load_result2.db has changed
--- 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
Binary file test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz has changed
Binary file test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi has changed
Binary file test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz has changed
Binary file test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi has changed
Binary file test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz has changed
Binary file test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi has changed
Binary file test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz has changed
Binary file test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi has changed
Binary file test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz has changed
Binary file test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi has changed