# HG changeset patch
# User iuc
# Date 1641321288 0
# Node ID 0de428c589f3feca4165617ba01949e9e180bd36
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
diff -r 000000000000 -r 0de428c589f3 load_annotations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/load_annotations.xml Tue Jan 04 18:34:48 2022 +0000
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+
+ as a collection
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+ python
+ pyyaml
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+ #set $elems=",".join(['{{"name": "%s", "ext": "%s", "filename": "{0}/%s", "dbkey": "{1}"}}' % (i, f, i) for i, f in zip($annotation, $annotation.fields.format.split(','))])
+ #set $elems=$elems.format($packaged_data.fields.path, $packaged_data.fields.dbkey)
+{"list_output": {"elements": [$elems]}}
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+ bool(str(retrieve_meta))
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+ `__
+accessible as a list of datasets collection.
+ ]]>
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diff -r 000000000000 -r 0de428c589f3 retrieve_meta.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/retrieve_meta.py Tue Jan 04 18:34:48 2022 +0000
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+
+import yaml
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser()
+
+ parser.add_argument('galaxy_json')
+ parser.add_argument(
+ '-o', '--ofile',
+ required=True
+ )
+ parser.add_argument(
+ '--format', choices=['yaml', 'tab'], default='yaml'
+ )
+ args = parser.parse_args()
+
+ galaxy_collection_info = json.load(open(args.galaxy_json))
+ annotation_info = next(iter(galaxy_collection_info.values()))['elements']
+ selected_ids = {i['name'] for i in annotation_info}
+ package_meta_file = os.path.join(
+ os.path.dirname(annotation_info[0]['filename']),
+ 'meta.yml'
+ )
+ meta = yaml.safe_load(open(package_meta_file))
+ meta['records'] = [
+ rec for rec in meta['records'] if rec['id'] in selected_ids
+ ]
+
+ with open(args.ofile, 'w') as fo:
+ if args.format == 'yaml':
+ yaml.dump(
+ meta, fo, allow_unicode=False, default_flow_style=False
+ )
+ else:
+ print('Annotation\tVersion', file=fo)
+ for record in meta['records']:
+ print(record['name'], record['version'], sep='\t', file=fo)
diff -r 000000000000 -r 0de428c589f3 test-data/anno-version.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/anno-version.tsv Tue Jan 04 18:34:48 2022 +0000
@@ -0,0 +1,3 @@
+Annotation Version
+CancerHotspots v2
+CIViC variants 01-Feb-2019
diff -r 000000000000 -r 0de428c589f3 test-data/packaged_annotation_data.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/packaged_annotation_data.loc Tue Jan 04 18:34:48 2022 +0000
@@ -0,0 +1,4 @@
+#
+#
+Cancer_variant_data__hg19__1__2021-12-16:hotspots.data.test hg19 CancerHotspots (v2, hg19; from Cancer variant data/vol:1/build2021-12-16) hotspots.data.test bed Cancer_variant_data__hg19__1__2021-12-16 Cancer variant data (hg19, vol:1/build:2021-12-16) ${__HERE__}/test-annotation-data
+Cancer_variant_data__hg19__1__2021-12-16:civic.variants.test hg19 CIViC variants (01-Feb-2019, hg19; from Cancer variant data/vol:1/build2021-12-16) civic.variants.test bed Cancer_variant_data__hg19__1__2021-12-16 Cancer variant data (hg19, vol:1/build:2021-12-16) ${__HERE__}/test-annotation-data
diff -r 000000000000 -r 0de428c589f3 test-data/test-annotation-data/civic.variants.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-annotation-data/civic.variants.test Tue Jan 04 18:34:48 2022 +0000
@@ -0,0 +1,7 @@
+1 11217229 11217230 https://civic.genome.wustl.edu/links/variants/543 MTOR
+1 11856377 11856378 https://civic.genome.wustl.edu/links/variants/258 MTHFR
+1 26211930 26232957 https://civic.genome.wustl.edu/links/variants/357 STMN1
+1 27022523 27108595 https://civic.genome.wustl.edu/links/variants/2108 ARID1A
+1 36932095 36933444 https://civic.genome.wustl.edu/links/variants/560 CSF3R
+1 40361097 40367685 https://civic.genome.wustl.edu/links/variants/670 MYCL
+1 57159475 57159478 https://civic.genome.wustl.edu/links/variants/385 PRKAA2
diff -r 000000000000 -r 0de428c589f3 test-data/test-annotation-data/hotspots.data.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-annotation-data/hotspots.data.test Tue Jan 04 18:34:48 2022 +0000
@@ -0,0 +1,12 @@
+1 2488104 2488105 TNFRSF14 0.0100655869328098
+1 2488105 2488106 TNFRSF14 0.0100655869328098
+1 2491288 2491289 TNFRSF14 0.0888304463274096
+1 2491289 2491290 TNFRSF14 0.0888304463274096
+1 8073431 8073432 ERRFI1 0.0212231821625514
+1 8073433 8073434 ERRFI1 0.0212231821625514
+1 8074312 8074313 ERRFI1 0.0452215429932304
+1 9779981 9779982 PIK3CD 0.0177652807514415
+1 9784112 9784113 PIK3CD 0.0656422395683915
+1 9784113 9784114 PIK3CD 0.0656422395683915
+1 9787029 9787030 PIK3CD 7.49932571758753e-06
+1 11169374 11169375 MTOR 2.29333311583453e-13
diff -r 000000000000 -r 0de428c589f3 test-data/test-annotation-data/meta.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-annotation-data/meta.yml Tue Jan 04 18:34:48 2022 +0000
@@ -0,0 +1,20 @@
+build: '2021-12-16'
+id: Cancer_variant_data__hg19__1__2021-12-16
+name: Cancer variant data
+records:
+- checksum: md5:ec8ec9afd4ae4935ac474e150e4e90aa
+ doi: 10.1158/2159-8290.CD-17-0321
+ format: bed
+ id: hotspots.data.test
+ name: CancerHotspots
+ source: https://zenodo.org/api/files/a89ff3af-261e-4c24-a9fb-5050ce8807b2/hotspots.bed
+ version: v2
+- checksum: md5:9e42bb7492be9e0011bf29b7e4f83f41
+ doi: http://dx.doi.org/10.1038/ng.3774
+ format: bed
+ id: civic.variants.test
+ name: CIViC variants
+ source: https://zenodo.org/api/files/a89ff3af-261e-4c24-a9fb-5050ce8807b2/01-Feb-2019-CIVic.bed
+ version: 01-Feb-2019
+refgenome: hg19
+volume: 1
diff -r 000000000000 -r 0de428c589f3 tool-data/packaged_annotation_data.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/packaged_annotation_data.loc.sample Tue Jan 04 18:34:48 2022 +0000
@@ -0,0 +1,20 @@
+#This file describes genome annotation data packages and their contents
+#available on the server.
+#Such data can consist of any number of individual files in a variety of
+#formats (e.g., bed, vcf, tabular) describing any features with respect to the
+#genome with the associated dbkey.
+#The directory referenced in the column of the table is expected to
+#contain the file listed under and a meta.yml file with details about
+#the annotation package volume and all of its contents.
+#This data table has the format (white space characters are TAB characters):
+#
+#
+#
+#So, packaged_annotation_data.loc tables could look like this:
+#
+#dbSNP_hg19__1__1:dbSNP.tidy hg19 dbSNP tidy (b147.20160601, hg19; from dbSNP/vol:1/build:1) dbSNP.tidy vcf_bgzip dbSNP__hg19__1__1 dbSNP (hg19, vol:1/build:1) /path/to/packaged_annotation_data/hg19/dbSNP/1/1
+#Cancer_variant_data__1__1:hotspots.data hg19 CancerHotspots (v2, hg19; from Cancer variant data/vol:1/build:1) hotspots.data bed Cancer_variant_data__hg19__1__1 Cancer variant data (hg19, vol:1/build:1) /path/to/packaged_annotation_data/hg19/Cancer_variant_data/1/1
+#Cancer_genes_data__1__1:civic.genes hg19 CIViC genes (01-Feb-2019, hg19; from Cancer gene data/vol:1/build:1) civic.genes tabular Cancer_gene_data__hg19__1__1 Cancer gene data (hg19, vol:1/build:1) /path/to/packaged_annotation_data/hg19/Cancer_variant_data/1/1
+#SARS-CoV-2_amplicon_primer_sets__NC_045512.2__1__1:ARTICv3 NC_045512.2 ARTIC (v3, NC_045512.2; from SARS-CoV-2 amplicon primer sets/vol:1/build:1) ARTICv3 bed6 SARS-CoV-2_amplicon_primer_sets__NC_045512.2__1__1 SARS-CoV-2 amplicon primer sets (NC_045512.2, vol:1/build:1) /path/to/packaged_annotation_data/NC_045512.2/SARS-CoV-2_amplicon_primer_sets/1/1
+#SARS-CoV-2_amplicon_primer_sets__NC_045512.2__1__1:ARTICv4 NC_045512.2 ARTIC (v4, NC_045512.2; from SARS-CoV-2 amplicon primer sets/vol:1/build:1) ARTICv4 bed6 SARS-CoV-2_amplicon_primer_sets__NC_045512.2__1__1 SARS-CoV-2 amplicon primer sets (NC_045512.2, vol:1/build:1) /path/to/packaged_annotation_data/NC_045512.2/SARS-CoV-2_amplicon_primer_sets/1/1
+#
diff -r 000000000000 -r 0de428c589f3 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Jan 04 18:34:48 2022 +0000
@@ -0,0 +1,7 @@
+
+
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+ value, dbkey, data_name, data_id, data_format, package_id, package_name, path
+
+
+
diff -r 000000000000 -r 0de428c589f3 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Tue Jan 04 18:34:48 2022 +0000
@@ -0,0 +1,7 @@
+
+
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+ value, dbkey, data_name, data_id, data_format, package_id, package_name, path
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+