Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq
changeset 17:0347d4d8b436 draft
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
| author | sanbi-uwc |
|---|---|
| date | Sat, 08 Sep 2018 08:48:38 -0400 |
| parents | d10b5e0ed486 |
| children | 75c1817c2ecf |
| files | data_manager/fetch_refseq.xml data_manager_conf.xml |
| diffstat | 2 files changed, 3 insertions(+), 19 deletions(-) [+] |
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--- a/data_manager/fetch_refseq.xml Sat Sep 08 04:19:52 2018 -0400 +++ b/data_manager/fetch_refseq.xml Sat Sep 08 08:48:38 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.17" tool_type="manage_data"> +<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.18" 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 04:19:52 2018 -0400 +++ b/data_manager_conf.xml Sat Sep 08 08:48:38 2018 -0400 @@ -9,25 +9,9 @@ <column name="path" output_ref="output_file" > <move type="file"> <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}"><![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}/${value}.fasta - ]]></target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">refseq/#echo str($dbkey).split('.')[1]#/${value}.fasta</target> </move> - <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}/${value}.fasta - ]]></value_translation> + <value_translation>refseq/#echo str($dbkey).split('.')[1]#/${value}.fasta</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>