Mercurial > repos > iuc > nanocompore_sampcomp
changeset 3:e7d7d87dc1a3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Wed, 01 Sep 2021 07:46:51 +0000 |
| parents | f657489960f7 |
| children | 89b4ed4145b3 |
| files | NanocomporeDB_process.py macros.xml sampcomp.xml test-data/KS_intensity_pvalue.bedgraph |
| diffstat | 4 files changed, 15 insertions(+), 5 deletions(-) [+] |
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--- a/NanocomporeDB_process.py Wed Jun 17 17:27:03 2020 +0000 +++ b/NanocomporeDB_process.py Wed Sep 01 07:46:51 2021 +0000 @@ -40,7 +40,7 @@ help='path to the annotations') parser.add_argument('--bedgraph', action="store_true", help='write output in BEDGRAPH format instead of BED') - parser.add_argument('--pvalue-threshold', default=1.0, + parser.add_argument('--pvalue-threshold', type=float, default=1.0, help='Maximum reported p-value.') parser.add_argument('--out-dir', default="./", type=is_valid_directory, help='path the plotting output directory.') @@ -52,9 +52,15 @@ print(db) print("DB read ids:", db.ref_id_list) + if args.bedgraph: + file_ext = 'bedgraph' + else: + file_ext = 'bed' + if args.annotation_bed: for pt in args.pvalue_types.split(','): - print("bedgraph output for p-value type:", pt) - db.save_to_bed(output_fn='{}/{}.bedgraph'.format(args.out_dir, pt), + out_path = '{}/{}.{}'.format(args.out_dir, pt, file_ext) + print("%s output for p-value type:" % out_path, pt) + db.save_to_bed(output_fn=out_path, pvalue_field=pt, pvalue_thr=args.pvalue_threshold, bedgraph=args.bedgraph)
--- a/macros.xml Wed Jun 17 17:27:03 2020 +0000 +++ b/macros.xml Wed Sep 01 07:46:51 2021 +0000 @@ -2,6 +2,11 @@ <macros> <token name="@TOOL_VERSION@">1.0.0rc3.post2</token> <token name="@DESCRIPTION@"></token> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">Nanocompore</xref> + </xrefs> + </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">nanocompore</requirement>
--- a/sampcomp.xml Wed Jun 17 17:27:03 2020 +0000 +++ b/sampcomp.xml Wed Sep 01 07:46:51 2021 +0000 @@ -1,6 +1,7 @@ <?xml version="1.0"?> <tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+galaxy0"> <description>to compare Nanopolished datasets</description> + <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros>