Mercurial > repos > dchristiany > frogs_data_manager
changeset 7:99b2dfb1fa1c draft
planemo upload commit c3ff1475af0e964a0c61458b66e2744c903d8d3d-dirty
| author | dchristiany |
|---|---|
| date | Fri, 04 Oct 2019 08:57:45 -0400 |
| parents | d11bc4a8f596 |
| children | cac51639c40f |
| files | data_manager/FROGS_data_manager.py data_manager/FROGS_data_manager.xml data_manager_conf.xml |
| diffstat | 3 files changed, 12 insertions(+), 12 deletions(-) [+] |
line wrap: on
line diff
--- a/data_manager/FROGS_data_manager.py Thu Oct 03 10:29:39 2019 -0400 +++ b/data_manager/FROGS_data_manager.py Fri Oct 04 08:57:45 2019 -0400 @@ -25,13 +25,14 @@ decoded_content = download.content.decode('utf-8') db_index = download.content.splitlines() db_index = [line.split("\t") for line in db_index[1:]] - db_index = [line[:4]+[line[1]+"_"+line[2]+"_"+line[1]]+[line[4]] for line in db_index] #add column name + db_index = [line[:4]+[line[1]+"_"+line[2]+"_"+line[3]]+[line[4]] for line in db_index] #add column name #get frogs dbs + os.chdir(target_directory) dir_name="frogs_db_"+time.strftime("%Y%m%d") os.mkdir(dir_name) dbs=set([]) - for line in db_index[:2]: + for line in db_index: value=line[4] name=value.replace("_"," ") link=line[5] @@ -84,7 +85,6 @@ phiX_sources(args.resource) #save info to json file - filename = args.output open(filename, 'wb').write(to_json_string(data_manager_dict)) if __name__ == "__main__":
--- a/data_manager/FROGS_data_manager.xml Thu Oct 03 10:29:39 2019 -0400 +++ b/data_manager/FROGS_data_manager.xml Fri Oct 04 08:57:45 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="FROGS_data_manager" name="FROGS Data manager" version="2019.10.03.1" tool_type="manage_data"> +<tool id="FROGS_data_manager" name="FROGS Data manager" version="2019.10.04" tool_type="manage_data"> <requirements> </requirements> <stdio>
--- a/data_manager_conf.xml Thu Oct 03 10:29:39 2019 -0400 +++ b/data_manager_conf.xml Fri Oct 04 08:57:45 2019 -0400 @@ -2,15 +2,15 @@ <data_managers> <data_manager tool_file="data_manager/FROGS_data_manager.xml" id="frogs_data_manager"> <data_table name="frogs_db"> - <output> - <column name="value"/> +<output> + <column name="value" /> <column name="name" /> - <column name="path" output_ref="output" > - <move type="directory"> + <column name="path" output_ref="output"> + <move type="directory" relativize_symlinks="False"> <source>#echo "/".join(str($path).split('/')[:-1])#</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">frogs_db</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">frogs_db/#echo str($path).split('/')[-2]#/</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/frogs_db/#echo "/".join(str($path).split('/')[-2:])#</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/#echo "/".join(str($path).split('/')[-2:])#</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> @@ -22,7 +22,7 @@ <column name="path" output_ref="output" > <move type="file"> <!--source>${path}/${value}.tsv</source--> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">HVL_db</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">HVL_db/</target> </move> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/HVL_db/${value}.fasta</value_translation> <value_translation type="function">abspath</value_translation> @@ -36,7 +36,7 @@ <column name="path" output_ref="output" > <move type="file"> <!--source>${path}/${value}.tsv</source--> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">phiX_db</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">phiX_db/</target> </move> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/phiX_db/${value}.fasta</value_translation> <value_translation type="function">abspath</value_translation>