Mercurial > repos > sanbi-uwc > data_manager_shapeit_reference
changeset 3:203133a92000 draft
planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 74cb5dd2b3aaed4a5b26840b451b8f2920e4b9fe-dirty
| author | sanbi-uwc |
|---|---|
| date | Thu, 13 Sep 2018 10:03:16 -0400 |
| parents | 495439e68fca |
| children | 094bd0114876 |
| files | data_manager/shapeit_ref.py data_manager/shapeit_ref.xml data_manager_conf.xml test-data/sample.out tool-data/shapeit_ref.loc.sample tool_data_table_conf.xml.sample tool_data_tables_conf.xml.sample |
| diffstat | 7 files changed, 13 insertions(+), 14 deletions(-) [+] |
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--- a/data_manager/shapeit_ref.py Thu Sep 13 08:47:41 2018 -0400 +++ b/data_manager/shapeit_ref.py Thu Sep 13 10:03:16 2018 -0400 @@ -52,7 +52,7 @@ exit("TAB character found in {} argument".format(column)) data_manager_dict = {} - data_table_entry = dict(key=args.key, description=args.description, path=args.path, + data_table_entry = dict(value=args.key, description=args.description, path=args.path, reference_prefix=args.reference_prefix, map_prefix=args.map_prefix) _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry)
--- a/data_manager/shapeit_ref.xml Thu Sep 13 08:47:41 2018 -0400 +++ b/data_manager/shapeit_ref.xml Thu Sep 13 10:03:16 2018 -0400 @@ -1,7 +1,7 @@ -<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.3"> +<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.4"> <command detect_errors="aggressive"><![CDATA[ python $__tool_directory__/shapeit_ref.py - '${key}' + '${value}' '${description}' '${path}' '${reference_prefix}' @@ -9,7 +9,7 @@ '${output_file}' ]]></command>> <inputs> - <param name="key" type="text" label="Short key to identify this reference set (no spaces)" /> + <param name="value" type="text" label="Short key to identify this reference set (no spaces)" /> <param name="description" type="text" label="Description of the reference data" /> <param name="path" type="text" label="Filesystem path to directory containing this reference set" /> <param name="reference_prefix" type="text" label="Filename prefix for the reference (.hap / .legend / .sample) files" />
--- a/data_manager_conf.xml Thu Sep 13 08:47:41 2018 -0400 +++ b/data_manager_conf.xml Thu Sep 13 10:03:16 2018 -0400 @@ -3,7 +3,7 @@ <data_manager tool_file="data_manager/shapeit_ref.xml" id="data_manager_shapeit_reference"> <data_table name="shapeit_ref"> <output> - <column name="key" /> + <column name="value" /> <column name="description" /> <column name="path" /> <column name="reference_prefix" />
--- a/test-data/sample.out Thu Sep 13 08:47:41 2018 -0400 +++ b/test-data/sample.out Thu Sep 13 10:03:16 2018 -0400 @@ -1,1 +1,1 @@ -{"data_tables": {"shapeit_ref": [{"description": "1000 Genomes Project (phase 3) haplotypes (http://mathgen.stats.ox.ac.uk/impute/1000GPX20Phase3.html)", "key": "1000GP_Phase3", "map_prefix": "genetic_map_", "path": "/tools/databases/1000G/1000GP_Phase3", "reference_prefix": "1000GP_Phase3_"}]}} +{"data_tables": {"shapeit_ref": [{"description": "1000 Genomes Project (phase 3) haplotypes (http://mathgen.stats.ox.ac.uk/impute/1000GPX20Phase3.html)", "value": "1000GP_Phase3", "map_prefix": "genetic_map_", "path": "/tools/databases/1000G/1000GP_Phase3", "reference_prefix": "1000GP_Phase3_"}]}}
--- a/tool-data/shapeit_ref.loc.sample Thu Sep 13 08:47:41 2018 -0400 +++ b/tool-data/shapeit_ref.loc.sample Thu Sep 13 10:03:16 2018 -0400 @@ -1,6 +1,6 @@ #This file lists the locations of SHAPEIT reference data connections # -#<unique_key> <description> <path> <reference_file_prefix> <map_file_prefix> +#<value> <description> <path> <reference_file_prefix> <map_file_prefix> # #For example #
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Sep 13 10:03:16 2018 -0400 @@ -0,0 +1,6 @@ +<tables> + <table name="shapeit_ref" comment_char="#"> + <columns>value, description, path, reference_prefix, map_prefix</columns> + <file path="tool-data/shapeit_ref.loc" /> + </table> +</tables> \ No newline at end of file
--- a/tool_data_tables_conf.xml.sample Thu Sep 13 08:47:41 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -<tables> - <!-- Locations of all fasta files under genome directory --> - <table name="shapeit_ref" comment_char="#"> - <columns>key, description, path, reference_prefix, map_prefix</columns> - <file path="tool-data/shapeit_ref.loc" /> - </table> -</tables> \ No newline at end of file