Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation

changeset 43:e42284a13168 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author scottx611x
date Fri, 08 Jul 2016 14:45:18 -0400
parents bf05cda04e1f
children f8cfca91827a
files data_manager_gene_annotation/data_manager/data_manager.py data_manager_gene_annotation/data_manager/gene_annotation_fetcher.xml data_manager_gene_annotation/data_manager_conf.xml
diffstat 3 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager_gene_annotation/data_manager/data_manager.py	Fri Jul 08 14:33:30 2016 -0400
+++ b/data_manager_gene_annotation/data_manager/data_manager.py	Fri Jul 08 14:45:18 2016 -0400
@@ -65,7 +65,7 @@
                 'value': gene_annotation_file_name.split(".")[0],
                 'dbkey': gene_annotation_file_name.split(".")[0],
                 'name': name,
-                'path': os.path.join(work_dir, gene_annotation_file_name)
+                'path': gene_annotation_file_name
             }
         }
     }
--- a/data_manager_gene_annotation/data_manager/gene_annotation_fetcher.xml	Fri Jul 08 14:33:30 2016 -0400
+++ b/data_manager_gene_annotation/data_manager/gene_annotation_fetcher.xml	Fri Jul 08 14:45:18 2016 -0400
@@ -17,9 +17,9 @@
     </command>
     <inputs>
         <param
-                help="Enter a unique identifier for the Data Table column to be created, or leave blank for an auto-generated uuid" label="Identifier for this DataTable entry" name="database_name" type="text" optional="True" />
+                help="Enter a descriptive name to be used in the tool drop-down menus" label="Identifier for this DataTable entry" name="database_name" type="text" optional="True" />
         <param
-                label="Enter URL pointing to a remote .gtf file" name="gene_annotation_url" type="text" optional="False"/>
+                label="Enter URL pointing to a remote GTF/GFF file" name="gene_annotation_url" type="text" optional="False"/>
     </inputs>
     <outputs>
         <data format="data_manager_json" name="out_file" />
--- a/data_manager_gene_annotation/data_manager_conf.xml	Fri Jul 08 14:33:30 2016 -0400
+++ b/data_manager_gene_annotation/data_manager_conf.xml	Fri Jul 08 14:45:18 2016 -0400
@@ -10,9 +10,10 @@
 				<column name="path" output_ref="out_file">
 					<move type="file">
 						<source>${path}</source>
-						<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">gene_annotations/${name}</target>
+						<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">
+							gene_annotations/${path}</target>
 					</move>
-					<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gene_annotations/${name}</value_translation>
+					<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gene_annotations/${path}</value_translation>
 					<value_translation type="function">abspath</value_translation>
 				</column>
 			</output>