From 155b198f8a7b09d4c5bf0e9c7742e3175d3dae12 Mon Sep 17 00:00:00 2001
From: Jayadev Joshi <jaidev53ster@gmail.com>
Date: Mon, 24 Feb 2025 10:31:41 -0500
Subject: [PATCH 1/3] Data-source tool for DICED databased added,
 DICED_Datasetbrowser.xml

---
 tools/data_source/DICED_Datasetbrowser.xml | 30 ++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 tools/data_source/DICED_Datasetbrowser.xml

diff --git a/tools/data_source/DICED_Datasetbrowser.xml b/tools/data_source/DICED_Datasetbrowser.xml
new file mode 100644
index 000000000000..3ae2350a6285
--- /dev/null
+++ b/tools/data_source/DICED_Datasetbrowser.xml
@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<!--
+    If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
+    the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
+    initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
+-->
+<tool name="DICED Database" id="DICED_table_direct1" tool_type="data_source" version="1.0.0">
+    <description>DICED is a web interface for access to proteolytic peptides</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="https://diced.lerner.ccf.org" check_values="false" method="post">
+        <display>go to DICED database $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
+        <param name="tool_id" type="hidden" value="DICED_table_direct1" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
+        <request_param galaxy_name="URL" remote_name="URL" missing="" />
+        <request_param galaxy_name="acc" remote_name="acc" missing="" />
+        <request_param galaxy_name="type" remote_name="type" missing="" />
+        <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
+        <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
+        <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
+        
+    </request_param_translation>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name}"/>
+    </outputs>
+</tool>
+

From 9fe917d352278c37cf0511862c493e988e327b6c Mon Sep 17 00:00:00 2001
From: Jayadev Joshi <jaidev53ster@gmail.com>
Date: Wed, 26 Feb 2025 10:00:40 -0500
Subject: [PATCH 2/3] tool_conf.xml.sample updated with new data source tool 
 DICED_Datasetbrowser.xml

---
 lib/galaxy/config/sample/tool_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/config/sample/tool_conf.xml.sample b/lib/galaxy/config/sample/tool_conf.xml.sample
index 7c7cbd6a2646..f2c2c0de1ca2 100644
--- a/lib/galaxy/config/sample/tool_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_conf.xml.sample
@@ -1,6 +1,7 @@
 <?xml version='1.0' encoding='utf-8'?>
 <toolbox monitor="true">
   <section id="getext" name="Get Data">
+    <tool file="data_source/DICED_Datasetbrowser.xml" />
     <tool file="data_source/upload.xml" />
     <tool file="data_source/ucsc_tablebrowser.xml" />
     <!-- <tool file="data_source/ucsc_tablebrowser_test.xml" /> -->

From 20ac054683062be7a653f19846a53004eebbd37b Mon Sep 17 00:00:00 2001
From: Jayadev Joshi <jaidev53ster@gmail.com>
Date: Thu, 27 Feb 2025 16:01:05 -0500
Subject: [PATCH 3/3] renamed the data source tool file

---
 lib/galaxy/config/sample/tool_conf.xml.sample             | 2 +-
 tools/data_source/{DICED_Datasetbrowser.xml => diced.xml} | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename tools/data_source/{DICED_Datasetbrowser.xml => diced.xml} (100%)

diff --git a/lib/galaxy/config/sample/tool_conf.xml.sample b/lib/galaxy/config/sample/tool_conf.xml.sample
index f2c2c0de1ca2..e76a0ec4eabc 100644
--- a/lib/galaxy/config/sample/tool_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_conf.xml.sample
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='utf-8'?>
 <toolbox monitor="true">
   <section id="getext" name="Get Data">
-    <tool file="data_source/DICED_Datasetbrowser.xml" />
+    <tool file="data_source/diced.xml" />
     <tool file="data_source/upload.xml" />
     <tool file="data_source/ucsc_tablebrowser.xml" />
     <!-- <tool file="data_source/ucsc_tablebrowser_test.xml" /> -->
diff --git a/tools/data_source/DICED_Datasetbrowser.xml b/tools/data_source/diced.xml
similarity index 100%
rename from tools/data_source/DICED_Datasetbrowser.xml
rename to tools/data_source/diced.xml