--- a/chatgpt.xml	Wed Sep 11 16:36:14 2024 +0000
+++ b/chatgpt.xml	Wed Jan 07 13:00:53 2026 +0000
@@ -1,80 +1,63 @@
-<tool id="chatgpt_openai_api" name="chatGPT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
+<tool id="chatgpt_openai_api" name="chatGPT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1">
     <description>Integrating OpenAI's ChatGPT into Galaxy</description>
     <macros>
-        <token name="@TOOL_VERSION@">2024</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@TOOL_VERSION@">2025</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
-        <requirement type="package" version="3.12">python</requirement>
-        <requirement type="package" version="1.35.13">openai</requirement>
+        <requirement type="package" version="3.13">python</requirement>
+        <requirement type="package" version="2.7.1">openai</requirement>
+        <credentials name="openai_credentials" version="1.0" label="OpenAI Credentials" description="Credentials for accessing OpenAI's API.">
+            <secret name="openai_api_key" inject_as_env="OPENAI_API_KEY" optional="false" label="OpenAI API Key" description="Your OpenAI API key is required to use this tool. You can obtain it from your OpenAI account dashboard."/>
+        </credentials>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #import json
 #import os
 #import re
 #set LINK_LIST = []
-#for $input in $context
-    #set file_name = os.path.splitext($input.element_identifier)[0]
-    ## list of supported filetypes in OpenAI. If Galaxy has a filetype that is not in this list, just use the generic `txt`.
-    #set ext = $input.ext if $input.ext in ['c', 'cpp', 'css', 'csv', 'docx', 'gif', 'html', 'java', 'jpeg', 'jpg', 'js', 'json', 'md', 'pdf', 'php', 'pkl', 'png', 'pptx', 'py', 'rb', 'tar', 'tex', 'ts', 'txt', 'webp', 'xlsx', 'xml', 'zip'] else 'txt'
-    #set LINK = re.sub('[^\w\-]', '_', $file_name)+'.'+$ext
-    ln -s '$input' '$LINK' &&
-    ## OpenAI has some special handling of "images", so let's annotate this here and pass it to the script
-    #set type = 'image' if $input.ext in ['jpg', 'jpeg', 'png', 'webp', 'gif'] else 'text'
-    $LINK_LIST.append([$LINK, $type])
-#end for
+#if $context
+    #for $input in $context
+        #set file_name = os.path.splitext($input.element_identifier)[0]
+        ## list of supported filetypes in OpenAI. If Galaxy has a filetype that is not in this list, just use the generic `txt`.
+        #set ext = $input.ext if $input.ext in ['c', 'cpp', 'css', 'csv', 'docx', 'gif', 'html', 'java', 'jpeg', 'jpg', 'js', 'json', 'md', 'pdf', 'php', 'pkl', 'png', 'pptx', 'py', 'rb', 'tar', 'tex', 'ts', 'txt', 'webp', 'xlsx', 'xml', 'zip'] else 'txt'
+        #set LINK = re.sub('[^\w\-]', '_', $file_name)+'.'+$ext
+        ln -s '$input' '$LINK' &&
+        ## OpenAI has some special handling of "images", so let's annotate this here and pass it to the script
+        #set type = 'image' if $input.ext in ['jpg', 'jpeg', 'png', 'webp', 'gif'] else 'text'
+        $LINK_LIST.append([$LINK, $type])
+    #end for
+#end if
 #set context_files = json.dumps($LINK_LIST)
 
 python '$__tool_directory__/chatgpt.py'
 '$context_files'
 '$prompt'
 '$model'
-'$openai_api_key_file'
     ]]></command>
-    <configfiles>
-        <configfile name="openai_api_key_file"><![CDATA[
-$__user__.extra_preferences.get('chatgpt|api_key', "")
-        ]]></configfile>
-    </configfiles>
     <inputs>
-        <conditional name="input_type">
-            <param name="input_type_selector" type="select" label="Choose the model" help="Vision models are capable to have image as input.">
-                <option value="vision" selected="true">Vision models</option>
-                <option value="all">All models</option>
-            </param>
-            <when value="vision">
-                <param name="model" type="select" optional="false" label="Model" help="Select the model you want to use.">
-                    <option value="gpt-4o-mini" selected="true">Affordable and intelligent small model for fast, lightweight tasks (gpt-4o-mini)</option>
-                    <option value="gpt-4o">High-intelligence flagship model for complex, multi-step tasks (gpt-4o)</option>
-                    <option value="gpt-4-turbo">The previous set of high-intelligence model with vision capabilities (gpt-4-turbo)</option>
-                </param>
-                <param name="context" type="data" multiple="true" optional="false" format="doc,docx,html,json,pdf,txt,jpg,jpeg,png,webp,gif" label="Context" max="500" help="This data will be uploaded to OpenAI's servers for processing."/>
-            </when>
-            <when value="all">
-                <param name="model" type="select" optional="false" label="Model" help="Select the model you want to use.">
-                    <option value="gpt-4o-mini" selected="true">Affordable and intelligent small model for fast, lightweight tasks (gpt-4o-mini)</option>
-                    <option value="gpt-4o">High-intelligence flagship model for complex, multi-step tasks (gpt-4o)</option>
-                    <option value="gpt-4-turbo">The previous set of high-intelligence model with vision capabilities (gpt-4-turbo)</option>
-                    <option value="gpt-4" selected="true">The previous set of high-intelligence model (gpt-4)</option>
-                    <option value="gpt-3.5-turbo">A fast, inexpensive model for simple tasks (GPT-3.5-turbo)</option>
-                </param>
-                <param name="context" type="data" multiple="true" optional="false" format="doc,docx,html,json,pdf,txt" label="Context" max="500" help="This data will be uploaded to OpenAI's servers for processing."/>
-            </when>
-        </conditional>
+        <param name="model" type="select" optional="false" label="Model" help="Select the model you want to use.">
+            <option value="gpt-5" selected="true">Flagship model for coding, reasoning, and agentic tasks across domains. (gpt-5)</option>
+            <option value="gpt-5-mini">Faster, more cost-efficient version of GPT-5. It's great for well-defined tasks and precise prompts. (gpt-5-mini)</option>
+            <option value="gpt-5-nano">Fastest, cheapest version of GPT-5. It's great for summarization and classification tasks. (gpt-5-nano)</option>
+            <option value="gpt-4.1">Excels at instruction following and tool calling, with broad knowledge across domains (gpt-4.1)</option>
+            <option value="gpt-4o">High-intelligence flagship model for complex, multi-step tasks (gpt-4o)</option>
+        </param>
+        <param name="context" type="data" multiple="true" optional="true" format="docx,html,json,pdf,txt,jpg,png,gif" label="Context" max="500" help="Optional context data that will be uploaded to OpenAI's servers for processing."/>
         <param name="prompt" type="text" optional="false" label="Prompt" help="Prompts or tasks you want ChatGPT to perform." area="true">
             <validator type="empty_field"/>
         </param>
     </inputs>
     <outputs>
-        <data name="output" format="txt" label="${tool.name} on ${on_string}" from_work_dir="./output.txt"/>
+        <data name="output" format="markdown" label="${tool.name} (${model}) #if $on_string then ' on ' + $on_string else ''#" from_work_dir="./output.md"/>
     </outputs>
     <tests>
         <test expect_failure="true" expect_exit_code="1">
+            <param name="model" value="gpt-5"/>
             <param name="context" value="chatgpt_test.txt" ftype="txt"/>
             <param name="prompt" value="What is this?"/>
-            <param name="model" value="gpt-4o-mini"/>
             <assert_stdout>
-                <has_text text="OpenAI API key is not provided in user preferences!"/>
+                <has_text text="OpenAI API key is not provided in credentials!"/>
             </assert_stdout>
         </test>
     </tests>
@@ -88,7 +71,7 @@
 Users can upload context data in various formats and ask questions or execute prompts related to that data.
 The tool then uploads the data to a OpenAI server and processes them using the selected ChatGPT model, returning an AI-generated response tailored to the context provided.
 
-To utilize this tool, users need to input their OpenAI API key in the user preferences. To obtain an API key, visit API keys page in your OpenAI Dashboard.
+To utilize this tool, users need to input their OpenAI API key in the credentials section. To obtain an API key, visit API keys page in your OpenAI Dashboard.
 Make sure to setup the payment method in your OpenAI account to use the API key.
 
 When you run this tool, your input data is sent to OpenAI's servers using your API-key. 
@@ -106,10 +89,10 @@
 
 **Input**
 
-1. **Upload Context Data**: Users can upload up to 500 files in formats such as DOC, DOCX, HTML, JSON, PDF, TXT, JPG, JPEG, PNG, WEBP, or GIF. 
-This context data serves as the input for the prompt you wish to execute.
+1. **Upload Context Data** (Optional): You can optionally upload up to 500 files in formats such as DOC, DOCX, HTML, JSON, PDF, TXT, JPG, JPEG, PNG, WEBP, or GIF. 
+This context data serves as the input for the prompt you wish to execute. If no context is provided, ChatGPT will respond based solely on the prompt.
 
-2. **Provide a Prompt**: Once the context data is added, users can provide a prompt for a task ChatGPT should execute.
+2. **Provide a Prompt**: Provide a prompt or task for ChatGPT to execute.
 The more specific the prompt, the more tailored the response will be.
 
 3. **Select a Model**: Choose the ChatGPT model that best fits your needs.