# HG changeset patch
# User estrain
# Date 1653860676 0
# Node ID 8897c156df99647e0fde941afe1004bed05bc54a
# Parent  dd5c2ac493865420c119f0c4b64d46c04b57a4a0
Uploaded

diff -r dd5c2ac49386 -r 8897c156df99 data_manager_fastani/data_manager/data_manager_fastani.py
--- a/data_manager_fastani/data_manager/data_manager_fastani.py	Sun May 29 20:51:41 2022 +0000
+++ b/data_manager_fastani/data_manager/data_manager_fastani.py	Sun May 29 21:44:36 2022 +0000
@@ -11,7 +11,7 @@
 import requests
 
 
-def download_D1(output_directory):
+def download_D1(output_directory,argsname):
 
     #FastANI databases from Kostas Lab 
     url="http://enve-omics.ce.gatech.edu/data/public_fastani/D1.tar.gz"
@@ -27,9 +27,12 @@
     tarcmd="tar xvzf D1.tar.gz; rm -Rf D1.tar.gz"
     os.system(tarcmd)
 
+    cmd="mv D1 " + argsname
+    os.system(cmd)
+
     os.chdir(cwd)    
    
-    return output_directory + "/D1/"
+    return output_directory + "/" + argsname 
 
 def download_VL(output_directory):
 
@@ -76,7 +79,7 @@
    
     parser = argparse.ArgumentParser(description='Download FastANI Databases')
     parser.add_argument('--type', type=str, required=True, nargs=1, help='Database Type')
-    parser.add_argument('--desc', type=str, required=True, nargs=1, help='Database Description')
+    parser.add_argument('--name', type=str, required=True, nargs=1, help='Unique Database Folder Name')
     parser.add_argument('--out', type=str, required=True, nargs=1, help='output file')
 
     args = parser.parse_args()
@@ -90,13 +93,13 @@
 
     #Fetch the files and build blast databases
     if(args.type[0]=="D1"):
-      output_directory=download_D1(output_directory)    
+      output_directory=download_D1(output_directory,args.name[0])    
       version="FastANI D1"
     elif(args.type[0]=="VL"): 
-      output_directory=download_D1(output_directory)    
+      output_directory=download_D1(output_directory,args.name[0])    
       output_directory=download_VL(output_directory)    
       version="FastANI D1 + VetLIRN"
       
-    print_json(version,output_directory,args.desc[0],args.out[0])
+    print_json(version,output_directory,args.name[0],args.out[0])
 
 if __name__ == "__main__": main()
diff -r dd5c2ac49386 -r 8897c156df99 data_manager_fastani/data_manager/data_manager_fastani.xml
--- a/data_manager_fastani/data_manager/data_manager_fastani.xml	Sun May 29 20:51:41 2022 +0000
+++ b/data_manager_fastani/data_manager/data_manager_fastani.xml	Sun May 29 21:44:36 2022 +0000
@@ -1,15 +1,16 @@
 <tool id="data_manager_fastani" name="FastANI Data Manger" tool_type="manage_data" version="0.0.1" profile="20.01">
     <requirements>
+        <requirement type="package">entrez-direct</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        python $__tool_directory__/data_manager_fastani.py --type $input_source_selector --desc $desc --out ${output_file};
+        python $__tool_directory__/data_manager_fastani.py --type $input_source_selector --name $name --out ${output_file};
     ]]></command>
     <inputs>
         <param name="input_source_selector" type="select" label="Database Selection">
           <option value="D1">FastANI D1</option>
           <option value="VL">FastANI D1 + VetLIRN Fish Pathogens</option>
         </param>
-        <param name="desc" type="text" format="text" label="Database Name"/> 
+        <param name="name" type="text" format="text" label="Database Name"/> 
     </inputs>
     <outputs>
         <data name="output_file" format="data_manager_json"/>
diff -r dd5c2ac49386 -r 8897c156df99 data_manager_fastani/data_manager_conf.xml
--- a/data_manager_fastani/data_manager_conf.xml	Sun May 29 20:51:41 2022 +0000
+++ b/data_manager_fastani/data_manager_conf.xml	Sun May 29 21:44:36 2022 +0000
@@ -3,12 +3,12 @@
     <data_manager tool_file="data_manager/data_manager_fastani.xml" id="data_manager_fastani">
       <data_table name="fastani">
         <output>
+          <column name="value" />
           <column name="name" />
-          <column name="description" />
           <column name="path" output_ref="output_file" >
             <move type="directory" relativize_symlinks="True">
               <src>${path}</src>
-              <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">fastani/${name}/</target>
+              <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">fastani/</target>
             </move>
             <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/fastani/${name}</value_translation>
             <value_translation type="function">abspath</value_translation>