# HG changeset patch
# User greg
# Date 1479924932 18000
# Node ID 54b4a38050eb3a16a1b73273794adbf9a2358cfc
# Parent  b96a5f7770dcf21988f4722fd37106b3c98a4e25
Uploaded

diff -r b96a5f7770dc -r 54b4a38050eb data_manager/data_manager_plant_tribes_scaffolds_download.xml
--- a/data_manager/data_manager_plant_tribes_scaffolds_download.xml	Wed Nov 23 13:15:21 2016 -0500
+++ b/data_manager/data_manager_plant_tribes_scaffolds_download.xml	Wed Nov 23 13:15:32 2016 -0500
@@ -9,32 +9,14 @@
             python $__tool_directory__/data_manager_plant_tribes_scaffolds_download.py
             --name "$name"
             --description "$description"
-            --data_source $data_source_cond.data_source
-            #if str($data_source_cond.data_source) == "web_url":
-                --web_url "$data_source_cond.web_url"
-            #else:
-                --file_system_paths "$data_source_cond.file_system_paths"
-                --create_symlink $data_source_cond.create_symlink
-            #end if
+            --web_url "$data_source_cond.web_url"
             --out_file "$out_file"
         ]]>
     </command>
     <inputs>
         <param name="name" type="text" value="" label="Data table entry unique ID"/>
         <param name="description" type="text" value="" label="Description of the data" help="Value is optional"/>
-        <conditional name="data_source_cond">
-            <param name="data_source" type="select" label="Choose the source for the Plant Tribes scaffolds files">
-                <option value="web_url" selected="true">Web URL</option>
-                <option value="file_system">File system paths</option>
-            </param>
-            <when value="web_url">
-                <param name="web_url" type="text" value="" label="Web URL" optional="False" />
-            </when>
-            <when value="file_system">
-                <param name="file_system_paths" type="text" value="" area="True" label="File system paths" optional="False" help="All files within the given folders and their sub-folders will be installed." />
-                <param name="create_symlink" type="boolean" truevalue="create_symlink" falsevalue="copy_file" label="Link files instead of copying" checked="false" />
-            </when>
-        </conditional>
+        <param name="web_url" type="text" value="" label="Web URL" optional="False" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json" />
@@ -47,24 +29,12 @@
 **What it does**
 
 This tool fetches scaffolds data used by the Plant Tribes Galaxy tools and populates the plant_tribes_scaffolds data table.
-
-The scaffolds data can be imported using a URL with an optional MD5 checksum or from files stored in a directory that is accessible to the Galaxy server.
-An optional description can be provided that will appear next to the scaffolds file name in the data table entry.
-
-------
-
-**Importing from a URL**
-
-Scaffolds data provided by the Floral Genome Project can be downloaded here:
+The scaffolds data can be imported using a URL, and an optional description can be provided that will appear next to the
+scaffolds file name in the data table entry.  Scaffolds data provided by the Floral Genome Project can be downloaded here:
 
  * 22 plant genomes (Angiosperms clusters, version 1.0):        http://fgp.huck.psu.edu/planttribes_data/22Gv1.0.tar.bz2
  * 22 plant genomes (Angiosperms clusters, version 1.1):        http://fgp.huck.psu.edu/planttribes_data/22Gv1.1.tar.bz2
 
-**Importing from file system paths**
-
-Use this option to import Plant Tribes scaffolds data if it is available on the Galaxy server's file system.  The value of
-each **File system paths** must be the root directory of the uncompressed and extracted scaffolds data.
-
     </help>
     <citations>
         <citation type="bibtex">