Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq
changeset 16:d10b5e0ed486 draft
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
| author | sanbi-uwc |
|---|---|
| date | Sat, 08 Sep 2018 04:19:52 -0400 |
| parents | 01ea53470921 |
| children | 0347d4d8b436 |
| files | data_manager/fetch_refseq.xml data_manager_conf.xml |
| diffstat | 2 files changed, 10 insertions(+), 2 deletions(-) [+] |
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--- a/data_manager/fetch_refseq.xml Sat Sep 08 03:46:26 2018 -0400 +++ b/data_manager/fetch_refseq.xml Sat Sep 08 04:19:52 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.16" tool_type="manage_data"> +<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.17" 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 Sat Sep 08 03:46:26 2018 -0400 +++ b/data_manager_conf.xml Sat Sep 08 04:19:52 2018 -0400 @@ -19,7 +19,15 @@ refseq/${release_num}/${value}.fasta ]]></target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/refseq/${dbkey}/${value}.fasta</value_translation> + <value_translation><![CDATA[ + #set name_parts = str($dbkey).split('.') + #if len($name_parts) == 3: + #set release_num = $name_parts[1] + #else + #set release_num = 'UNKNOWN_RELEASE' + #end if + refseq/${release_num}/${value}.fasta + ]]></value_translation> <value_translation type="function">abspath</value_translation> </column> </output>