Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq
changeset 13:dd9f976e9d97 draft
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
| author | sanbi-uwc |
|---|---|
| date | Sat, 08 Sep 2018 03:08:02 -0400 |
| parents | 45baee31ca39 |
| children | 1977080c99ec |
| files | data_manager/fetch_refseq.py data_manager/fetch_refseq.xml data_manager_conf.xml |
| diffstat | 3 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/fetch_refseq.py Fri Sep 07 20:14:04 2018 -0400 +++ b/data_manager/fetch_refseq.py Sat Sep 08 03:08:02 2018 -0400 @@ -149,7 +149,7 @@ if args.galaxy_datamanager_filename is not None: for i, mol_type in enumerate(mol_types): assert mol_type in fasta_files[i], "Filename does not contain expected mol_type ({}, {})".format(mol_type, fasta_files[i]) - unique_key = division_name + '.' + release_num + '.' + mol_type + '.' + today_str + unique_key = division_name + '.' + release_num + '.' + mol_type # note: this is now same as dbkey dbkey = division_name + '.' + release_num + '.' + mol_type desc = 'RefSeq ' + division_name + ' Release ' + release_num + ' ' + mol_type + ' (' + today_str + ')' path = os.path.join(output_directory, fasta_files[i])
--- a/data_manager/fetch_refseq.xml Fri Sep 07 20:14:04 2018 -0400 +++ b/data_manager/fetch_refseq.xml Sat Sep 08 03:08:02 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.13" tool_type="manage_data"> +<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.14" tool_type="manage_data"> <description>Fetch FASTA data from NCBI RefSeq and update all_fasta data table</description> <requirements> <requirement type="package" version="3">python</requirement>
--- a/data_manager_conf.xml Fri Sep 07 20:14:04 2018 -0400 +++ b/data_manager_conf.xml Sat Sep 08 03:08:02 2018 -0400 @@ -9,7 +9,10 @@ <column name="path" output_ref="output_file" > <move type="file"> <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">refseq/${dbkey}/${value}.fasta</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}"><![CDATA[ + #set release_num = str($dbkey).split()[1] + refseq/${release_num}/${value}.fasta + ]]></target> </move> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/refseq/${dbkey}/${value}.fasta</value_translation> <value_translation type="function">abspath</value_translation>