Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder
changeset 8:56686a746b91 draft
planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit dc358455cd2140328ddbb9f8f2e221f8121c6b7b
| author | sanbi-uwc |
|---|---|
| date | Thu, 11 Feb 2016 06:56:21 -0500 |
| parents | 0ff626afce84 |
| children | ccb7ce1ad9b3 |
| files | data_manager/rnastar_index_builder.py data_manager/rnastar_index_builder.xml data_manager_conf.xml tool-data/rnastar_index.loc.sample tool-data/rnastar_indexes.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 6 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager/rnastar_index_builder.py Wed Feb 10 08:29:45 2016 -0500 +++ b/data_manager/rnastar_index_builder.py Thu Feb 11 06:56:21 2016 -0500 @@ -56,7 +56,7 @@ parser.add_argument('--fasta_filename') parser.add_argument('--fasta_dbkey') parser.add_argument('--fasta_description', default=None) -parser.add_argument('--data_table_name', default='rnastar_indexes') +parser.add_argument('--data_table_name', default='rnastar_index') args = parser.parse_args() filename = args.output_filename
--- a/data_manager/rnastar_index_builder.xml Wed Feb 10 08:29:45 2016 -0500 +++ b/data_manager/rnastar_index_builder.xml Thu Feb 11 06:56:21 2016 -0500 @@ -4,7 +4,7 @@ <requirements> <requirement type="package" version="2.4.0d">rnastar</requirement> </requirements> - <command interpreter="python">rnastar_index_builder.py "${out_file}" --fasta_filename "${input1.fields.path}" --fasta_dbkey "${input1.fields.dbkey}" --fasta_description "${input1.fields.name}" --data_table_name "rnastar_indexes"</command> + <command interpreter="python">rnastar_index_builder.py "${out_file}" --fasta_filename "${input1.fields.path}" --fasta_dbkey "${input1.fields.dbkey}" --fasta_description "${input1.fields.name}" --data_table_name "rnastar_index"</command> <inputs> <param name="input1" type="select" label="Genome to index(FASTA format)"> <options from_data_table="all_fasta"/>
--- a/data_manager_conf.xml Wed Feb 10 08:29:45 2016 -0500 +++ b/data_manager_conf.xml Thu Feb 11 06:56:21 2016 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="utf-8" ?> <data_managers> <data_manager tool_file="data_manager/rnastar_index_builder.xml" id="rnastar_index_builder" version="0.0.1"> - <data_table name="rnastar_indexes"> + <data_table name="rnastar_index"> <output> <column name="value" /> <column name="dbkey" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rnastar_index.loc.sample Thu Feb 11 06:56:21 2016 -0500 @@ -0,0 +1,2 @@ +#TODO: Document +#<unique_build_id> <dbkey> <display_name> <directory_path>
--- a/tool-data/rnastar_indexes.loc.sample Wed Feb 10 08:29:45 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -#TODO: Document -#<unique_build_id> <dbkey> <display_name> <directory_path>
--- a/tool_data_table_conf.xml.sample Wed Feb 10 08:29:45 2016 -0500 +++ b/tool_data_table_conf.xml.sample Thu Feb 11 06:56:21 2016 -0500 @@ -1,6 +1,6 @@ <tables> - <table name="rnastar_indexes.loc" comment_char="#"> + <table name="rnastar_index" comment_char="#"> <columns>value, dbkey, name, path</columns> - <file path="tool-data/rnastar_indexes.loc" /> + <file path="tool-data/rnastar_index.loc" /> </table> </tables>