# HG changeset patch
# User iuc
# Date 1490803749 14400
# Node ID 13c235ded82e9e7f66507945fa4cbb6842bd3da5
# Parent  80b0bd65cbfbc197de7b051b4abc0872d90afe49
Uploaded

diff -r 80b0bd65cbfb -r 13c235ded82e data_manager/data_manager_plant_tribes_scaffolds_download.xml
--- a/data_manager/data_manager_plant_tribes_scaffolds_download.xml	Wed Mar 29 12:08:57 2017 -0400
+++ b/data_manager/data_manager_plant_tribes_scaffolds_download.xml	Wed Mar 29 12:09:09 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_plant_tribes_scaffolds_download" name="PlantTribes Scaffolds Download" version="1.0.0" tool_type="manage_data">
+<tool id="data_manager_plant_tribes_scaffolds_download" name="PlantTribes Scaffolds Download" version="1.1.0" tool_type="manage_data">
     <description></description>
     <stdio>
         <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
@@ -7,16 +7,18 @@
     <command>
         <![CDATA[
             python $__tool_directory__/data_manager_plant_tribes_scaffolds_download.py
-            --name "$name"
-            --description "$description"
-            --web_url "$web_url"
-            --out_file "$out_file"
+            --name '$name'
+            --description '$description'
+            --web_url '$web_url'
+            --config_web_url '$config_web_url'
+            --out_file '$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"/>
-        <param name="web_url" type="text" value="" label="Web URL" optional="False" />
+        <param name="web_url" type="text" value="" label="URL for downloading scaffolds" help="Must be same version as configs" optional="False" />
+        <param name="config_web_url" type="text" value="" label="URL for downloading configs" help="Must be same version as scaffolds" optional="False" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json" />
@@ -28,13 +30,20 @@
 
 **What it does**
 
-This tool fetches scaffolds data used by the PlantTribes Galaxy tools and populates the plant_tribes_scaffolds data table.
-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:
+This tool fetches scaffolds data and default configuration files used by the PlantTribes Galaxy tools and populates the
+plant_tribes_scaffolds data table.  Both the scaffolds data and the default configuration files 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 using these URLs:
 
  * 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
 
+Default configuration files provided by the Floral Genome Project can be downloaded using these URLs:
+
+ * 22 plant genomes (Angiosperms clusters, version 1.0):        http://fgp.huck.psu.edu/planttribes_config/22Gv1.0.tar.gz
+ * 22 plant genomes (Angiosperms clusters, version 1.1):        http://fgp.huck.psu.edu/planttribes_config/22Gv1.1.tar.gz
+ 
     </help>
     <citations>
         <citation type="bibtex">
@@ -43,7 +52,7 @@
             title = {None},
             year = {None},
             eprint = {None},
-            url = {None}
+            url = {https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader}
         }</citation>
     </citations>
 </tool>