Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder
changeset 10:61084615bb57 draft
planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit ab936cfb63040f3e5d34d35c1e2b968698fd2caa
| author | sanbi-uwc |
|---|---|
| date | Mon, 15 Feb 2016 03:21:58 -0500 |
| parents | ccb7ce1ad9b3 |
| children | 6096741e8d83 |
| files | data_manager/rnastar_index_builder.py data_manager/rnastar_index_builder.xml data_manager_conf.xml |
| diffstat | 3 files changed, 1 insertions(+), 11 deletions(-) [+] |
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--- a/data_manager/rnastar_index_builder.py Fri Feb 12 03:30:43 2016 -0500 +++ b/data_manager/rnastar_index_builder.py Mon Feb 15 03:21:58 2016 -0500 @@ -62,7 +62,6 @@ filename = args.output_filename params = load(open(filename, 'rb')) -print(params) output_directory = params[ 'output_data' ][0]['extra_files_path'] makedirs( output_directory ) data_manager_dict = {}
--- a/data_manager/rnastar_index_builder.xml Fri Feb 12 03:30:43 2016 -0500 +++ b/data_manager/rnastar_index_builder.xml Mon Feb 15 03:21:58 2016 -0500 @@ -11,15 +11,6 @@ </param> <param type="text" name="sequence_name" value="" label="Name of sequence" /> <param type="text" name="sequence_id" value="" label="ID for sequence" /> - <!--<conditional name="advanced_options">--> - <!--<param name="show_advanced_options" type="boolean" label="Show advanced options?"--> - <!--truevalue="yes" falsevalue="no" checked="false" />--> - <!--<when value="yes">--> - <!--<param name="chr_bin_nbits" type="integer" label="Scale of chromosome bins"--> - <!--help="value is log2(chrBin), where chrBin is the size of the bins for genome storage: each chromosome will occupy an integer number of bins" default="18" />--> - <!--</when>--> - <!--<when value="no" />--> - <!--</conditional>--> </inputs> <outputs> <data name="out_file" format="data_manager_json" />
--- a/data_manager_conf.xml Fri Feb 12 03:30:43 2016 -0500 +++ b/data_manager_conf.xml Mon Feb 15 03:21:58 2016 -0500 @@ -5,7 +5,7 @@ <output> <column name="value" /> <column name="dbkey" /> - <column name="path" output_ref="out_dir"> + <column name="path" output_ref="out_file"> <move type="directory" relative_symlinks="True"> <!-- no need to set source, gets taken from out_dir.extra_files_path --> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/rnastar_index/${value}</target>