# HG changeset patch
# User sanbi-uwc
# Date 1536390482 14400
# Node ID dd9f976e9d97ecfff074577c0c1a5dc4dd3500b6
# Parent  45baee31ca39bbb5b46df42bae9ce279c89c01ad
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty

diff -r 45baee31ca39 -r dd9f976e9d97 data_manager/fetch_refseq.py
--- 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])
diff -r 45baee31ca39 -r dd9f976e9d97 data_manager/fetch_refseq.xml
--- 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>
diff -r 45baee31ca39 -r dd9f976e9d97 data_manager_conf.xml
--- 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>