Mercurial > repos > iuc > data_manager_salmon_index_builder
changeset 3:6437fc47878f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 5f199df1a4ce3c569c3778e3eb67019fc1b0c8db"
| author | iuc |
|---|---|
| date | Sun, 27 Sep 2020 09:03:26 +0000 |
| parents | 57274fe5e01a |
| children | 566207ae614c |
| files | data_manager/salmon_index_builder.py data_manager/salmon_index_builder.xml |
| diffstat | 2 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager/salmon_index_builder.py Thu Nov 28 15:48:04 2019 -0500 +++ b/data_manager/salmon_index_builder.py Sun Sep 27 09:03:26 2020 +0000 @@ -27,7 +27,7 @@ def build_salmon_index(data_manager_dict, options, params, sequence_id, sequence_name): data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME - target_directory = params['output_data' ][0]['extra_files_path'] + target_directory = params['output_data'][0]['extra_files_path'] if not os.path.exists(target_directory): os.mkdir(target_directory) args = ['salmon', 'index']
--- a/data_manager/salmon_index_builder.xml Thu Nov 28 15:48:04 2019 -0500 +++ b/data_manager/salmon_index_builder.xml Sun Sep 27 09:03:26 2020 +0000 @@ -1,11 +1,11 @@ -<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.14.1" profile="19.01"> +<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="1.3.0" profile="19.01"> <description>index builder</description> <requirements> - <requirement type="package" version="0.14.1">salmon</requirement> + <requirement type="package" version="1.3.0">salmon</requirement> <requirement type="package" version="3.7">python</requirement> </requirements> <macros> - <token name="@IDX_VERSION@">q6</token> + <token name="@IDX_VERSION@">q7</token> </macros> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}' @@ -36,7 +36,7 @@ <param name="sequence_id" value="sequence_id"/> <output name="out_file"> <assert_contents> - <has_line line='{"data_tables": {"salmon_indexes_versioned": [{"dbkey": "phiX174", "name": "sequence_name", "path": "sequence_id", "value": "sequence_id", "version": "q6"}]}}' /> + <has_line line='{"data_tables": {"salmon_indexes_versioned": [{"dbkey": "phiX174", "name": "sequence_name", "path": "sequence_id", "value": "sequence_id", "version": "q7"}]}}' /> </assert_contents> </output> </test>