Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
changeset 12:680110ffdcfe draft
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
| author | rhpvorderman |
|---|---|
| date | Mon, 11 Sep 2017 07:33:51 -0400 |
| parents | 8ccfeedd1f03 |
| children | 0a1afc109ad9 |
| files | data_manager/data_manager_select_index_by_path.xml data_manager/indexes.yml data_manager/path_name_value_key_manager.py test.json |
| diffstat | 4 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager/data_manager_select_index_by_path.xml Mon Sep 11 07:23:55 2017 -0400 +++ b/data_manager/data_manager_select_index_by_path.xml Mon Sep 11 07:33:51 2017 -0400 @@ -15,7 +15,7 @@ <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." /> <param name="path" type="text" value="" label="path field for the entry" /> <param name="data_table" type="select" value="" label="data table for the index"> - <option value='all_fasta --no_prefix'>all_fasta</option> + <option value='all_fasta'>all_fasta</option> <option value='bowtie2_indexes'>bowtie2_indexes</option> <option value='bowtie_indexes'>bowtie_indexes</option> <option value='bowtie_indexes_color'>bowtie_indexes_color</option> @@ -25,7 +25,7 @@ <option value='gatk_picard_indexes'>gatk_picard_indexes</option> <option value='gene_transfer'>gene_transfer</option> <option value='hisat2_indexes'>hisat2_indexes</option> - <option value='kallisto_indexes --no-prefix'>kallisto_indexes</option> + <option value='kallisto_indexes'>kallisto_indexes</option> <option value='picard_indexes'>picard_indexes</option> <option value='tophat2_indexes'>tophat2_indexes</option> </param>
--- a/data_manager/indexes.yml Mon Sep 11 07:23:55 2017 -0400 +++ b/data_manager/indexes.yml Mon Sep 11 07:33:51 2017 -0400 @@ -2,6 +2,7 @@ name: fasta file extensions: - .fa + no_prefix: True bowtie2_indexes: name: bowtie2 index extensions: @@ -40,6 +41,7 @@ - .ht2 kallisto_indexes: name: kallisto index + no_prefix: True picard_indexes: name: picard index tophat2_indexes:
--- a/data_manager/path_name_value_key_manager.py Mon Sep 11 07:23:55 2017 -0400 +++ b/data_manager/path_name_value_key_manager.py Mon Sep 11 07:33:51 2017 -0400 @@ -58,7 +58,6 @@ parser.add_argument( '--path', action='store', type=str, default=None, help='path' ) parser.add_argument( '--data_table_name', action='store', type=str, default=None, help='path' ) parser.add_argument( '--json_output_file', action='store', type=str, default=None, help='path' ) - parser.add_argument( '--no_prefix', action='store_true', help='Does not check the prefix but checks the path. Useful for indexes that reference a single file.') options = parser.parse_args() path = check_param("path", options.path) @@ -75,7 +74,8 @@ index_dict = indexes.get(data_table_name,{}) index_name = index_dict.get('name','index') index_extensions = index_dict.get('extensions', ['']) - if not options.no_prefix: + no_prefix = index_dict.get('no_prefix', False) + if not no_prefix: dirname = os.path.dirname(path) prefix = basename for extension in index_extensions:
--- a/test.json Mon Sep 11 07:23:55 2017 -0400 +++ b/test.json Mon Sep 11 07:33:51 2017 -0400 @@ -1,1 +1,1 @@ -{"data_tables": {"fasta_indexes": [{"path": "test-data/sam_indexes/EboVir3.fa", "dbkey": "EboVir3", "name": "EboVir3", "value": "EboVir3"}]}} +{"data_tables": {"all_fasta": [{"path": "test-data/EboVir3.fa", "dbkey": "EboVir3", "name": "EboVir3", "value": "EboVir3"}]}}