# HG changeset patch
# User dchristiany
# Date 1570193865 14400
# Node ID 99b2dfb1fa1c1fc745ebb52fd2db17f02ad530ee
# Parent  d11bc4a8f596d290b25ace1d4ef80319e1f0a81c
planemo upload commit c3ff1475af0e964a0c61458b66e2744c903d8d3d-dirty

diff -r d11bc4a8f596 -r 99b2dfb1fa1c data_manager/FROGS_data_manager.py
--- a/data_manager/FROGS_data_manager.py	Thu Oct 03 10:29:39 2019 -0400
+++ b/data_manager/FROGS_data_manager.py	Fri Oct 04 08:57:45 2019 -0400
@@ -25,13 +25,14 @@
         decoded_content = download.content.decode('utf-8')
         db_index = download.content.splitlines()    
         db_index = [line.split("\t") for line in db_index[1:]]
-        db_index = [line[:4]+[line[1]+"_"+line[2]+"_"+line[1]]+[line[4]] for line in db_index]  #add column name
+        db_index = [line[:4]+[line[1]+"_"+line[2]+"_"+line[3]]+[line[4]] for line in db_index]  #add column name
 
     #get frogs dbs
+    os.chdir(target_directory)
     dir_name="frogs_db_"+time.strftime("%Y%m%d")
     os.mkdir(dir_name)
     dbs=set([])
-    for line in db_index[:2]:
+    for line in db_index:
         value=line[4]
         name=value.replace("_"," ")
         link=line[5]
@@ -84,7 +85,6 @@
         phiX_sources(args.resource)
 
     #save info to json file
-    filename = args.output
     open(filename, 'wb').write(to_json_string(data_manager_dict))
 
 if __name__ == "__main__":
diff -r d11bc4a8f596 -r 99b2dfb1fa1c data_manager/FROGS_data_manager.xml
--- a/data_manager/FROGS_data_manager.xml	Thu Oct 03 10:29:39 2019 -0400
+++ b/data_manager/FROGS_data_manager.xml	Fri Oct 04 08:57:45 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="FROGS_data_manager" name="FROGS Data manager" version="2019.10.03.1" tool_type="manage_data">
+<tool id="FROGS_data_manager" name="FROGS Data manager" version="2019.10.04" tool_type="manage_data">
     <requirements>
     </requirements>
     <stdio>
diff -r d11bc4a8f596 -r 99b2dfb1fa1c data_manager_conf.xml
--- a/data_manager_conf.xml	Thu Oct 03 10:29:39 2019 -0400
+++ b/data_manager_conf.xml	Fri Oct 04 08:57:45 2019 -0400
@@ -2,15 +2,15 @@
 <data_managers>
     <data_manager tool_file="data_manager/FROGS_data_manager.xml" id="frogs_data_manager">
         <data_table name="frogs_db">
-            <output>
-                <column name="value"/>
+<output>
+                <column name="value" />
                 <column name="name" />
-                <column name="path" output_ref="output" >
-                    <move type="directory">
+                <column name="path" output_ref="output">
+                    <move type="directory" relativize_symlinks="False">
                         <source>#echo "/".join(str($path).split('/')[:-1])#</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">frogs_db</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">frogs_db/#echo str($path).split('/')[-2]#/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/frogs_db/#echo "/".join(str($path).split('/')[-2:])#</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/#echo "/".join(str($path).split('/')[-2:])#</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -22,7 +22,7 @@
                 <column name="path" output_ref="output" >
                     <move type="file">
                         <!--source>${path}/${value}.tsv</source-->
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">HVL_db</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">HVL_db/</target>
                     </move>
                     <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/HVL_db/${value}.fasta</value_translation>
                     <value_translation type="function">abspath</value_translation>
@@ -36,7 +36,7 @@
                 <column name="path" output_ref="output" >
                     <move type="file">
                         <!--source>${path}/${value}.tsv</source-->
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">phiX_db</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">phiX_db/</target>
                     </move>
                     <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/phiX_db/${value}.fasta</value_translation>
                     <value_translation type="function">abspath</value_translation>