Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation

changeset 34:30039ecf0da0 draft

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planemo upload
author scottx611x
date Thu, 23 Jun 2016 17:09:05 -0400
parents bfc662f13436
children 355ecb4aaffd
files data_manager_gene_annotation/data_manager/data_manager.py data_manager_gene_annotation/data_manager_conf.xml
diffstat 2 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager_gene_annotation/data_manager/data_manager.py	Thu Jun 23 17:01:45 2016 -0400
+++ b/data_manager_gene_annotation/data_manager/data_manager.py	Thu Jun 23 17:09:05 2016 -0400
@@ -63,8 +63,8 @@
             'gene_annotation': {
                 'value': str(datetime.datetime.now()),
                 'dbkey': str(args.name),
-                'name': gene_annotation_file_name.split(".")[0],
-                'path': gene_annotation_file_name
+                'name': gene_annotation_file_name,
+                'path': os.path.join(os.getcwd(), gene_annotation_file_name)
             }
         }
     }
--- a/data_manager_gene_annotation/data_manager_conf.xml	Thu Jun 23 17:01:45 2016 -0400
+++ b/data_manager_gene_annotation/data_manager_conf.xml	Thu Jun 23 17:09:05 2016 -0400
@@ -10,9 +10,9 @@
 				<column name="path" output_ref="out_file">
 					<move type="file" relativize_symlinks="False">
 						<source>${path}</source>
-						<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/gene_annotations/${path}</target>
+						<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/gene_annotations/${name}</target>
 					</move>
-					<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/gene_annotations/${path}</value_translation>
+					<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/gene_annotations/${name}</value_translation>
 					<value_translation type="function">abspath</value_translation>
 				</column>
 			</output>