Mercurial > repos > iuc > data_manager_star_index_builder
changeset 2:f537d3e00eb8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 811025ef8d9f60f4b02d66f7218127669fb42e0b
| author | iuc |
|---|---|
| date | Fri, 23 Jun 2017 04:26:07 -0400 |
| parents | cdc4d8a998e1 |
| children | 50ca9af6db2e |
| files | data_manager/rna_star_index_builder.py data_manager_conf.xml tool-data/rnastar_index2.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager/rna_star_index_builder.py Fri Apr 21 12:36:31 2017 -0400 +++ b/data_manager/rna_star_index_builder.py Fri Jun 23 04:26:07 2017 -0400 @@ -22,7 +22,7 @@ if options.withGTF: withGTF = "1" - data_manager_dict = {'data_tables': {options.data_table: [dict( value=options.value, dbkey=options.dbkey, name=options.name, path=options.subdir, withGTF=withGTF )]}} + data_manager_dict = {'data_tables': {options.data_table: [dict({"value": options.value, "dbkey": options.dbkey, "name": options.name, "path": options.subdir, "with-gtf": withGTF} )]}} open( options.config_file, 'wb' ).write( json.dumps( data_manager_dict ) )
--- a/data_manager_conf.xml Fri Apr 21 12:36:31 2017 -0400 +++ b/data_manager_conf.xml Fri Jun 23 04:26:07 2017 -0400 @@ -17,7 +17,7 @@ <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/rnastar_index2/${value}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> - <column name="withGTF" /> + <column name="with-gtf" /> </output> </data_table> </data_manager>
--- a/tool-data/rnastar_index2.loc.sample Fri Apr 21 12:36:31 2017 -0400 +++ b/tool-data/rnastar_index2.loc.sample Fri Jun 23 04:26:07 2017 -0400 @@ -5,9 +5,9 @@ #the directories in which those files are stored. The rnastar_index2.loc #file has this format (longer white space characters are TAB characters): # -#<unique_build_id> <dbkey> <display_name> <file_base_path> <withGTF> +#<unique_build_id> <dbkey> <display_name> <file_base_path> <with-gtf> # -#The <with_gtf> column should be 1 or 0, indicating whether the index was made +#The <with-gtf> column should be 1 or 0, indicating whether the index was made #with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not, #respecively. #
--- a/tool_data_table_conf.xml.sample Fri Apr 21 12:36:31 2017 -0400 +++ b/tool_data_table_conf.xml.sample Fri Jun 23 04:26:07 2017 -0400 @@ -6,7 +6,7 @@ </table> <!-- Locations of indexes in the BWA mapper format --> <table name="rnastar_index2" comment_char="#" allow_duplicate_entries="False"> - <columns>value, dbkey, name, path, withGTF</columns> + <columns>value, dbkey, name, path, with-gtf</columns> <file path="tool-data/rnastar_index2.loc" /> </table> </tables>