Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation

changeset 44:f8cfca91827a draft

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planemo upload
author scottx611x
date Fri, 08 Jul 2016 14:54:06 -0400
parents e42284a13168
children 16e961b2f35c
files data_manager_gene_annotation/data_manager/data_manager.py data_manager_gene_annotation/data_manager_conf.xml
diffstat 2 files changed, 5 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager_gene_annotation/data_manager/data_manager.py	Fri Jul 08 14:45:18 2016 -0400
+++ b/data_manager_gene_annotation/data_manager/data_manager.py	Fri Jul 08 14:54:06 2016 -0400
@@ -62,10 +62,10 @@
     data_manager_entry = {
         'data_tables': {
             'gene_annotation': {
-                'value': gene_annotation_file_name.split(".")[0],
+                'value': gene_annotation_file_name,
                 'dbkey': gene_annotation_file_name.split(".")[0],
                 'name': name,
-                'path': gene_annotation_file_name
+                'path': os.path.join(work_dir, gene_annotation_file_name)
             }
         }
     }
--- a/data_manager_gene_annotation/data_manager_conf.xml	Fri Jul 08 14:45:18 2016 -0400
+++ b/data_manager_gene_annotation/data_manager_conf.xml	Fri Jul 08 14:54:06 2016 -0400
@@ -9,11 +9,12 @@
 				<column name="name" />
 				<column name="path" output_ref="out_file">
 					<move type="file">
-						<source>${path}</source>
+						<source>${value}</source>
 						<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">
 							gene_annotations/${path}</target>
 					</move>
-					<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gene_annotations/${path}</value_translation>
+					<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH
+					}/gene_annotations/${value}</value_translation>
 					<value_translation type="function">abspath</value_translation>
 				</column>
 			</output>