# HG changeset patch
# User sanbi-uwc
# Date 1536394792 14400
# Node ID d10b5e0ed486c260465db75d8468f020694c8334
# Parent  01ea534709218c1fc3cf7eef93c8e5bf70a54686
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty

diff -r 01ea53470921 -r d10b5e0ed486 data_manager/fetch_refseq.xml
--- 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>
diff -r 01ea53470921 -r d10b5e0ed486 data_manager_conf.xml
--- 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>