annotate chat_analysis.xml @ 4:dd4874a77f62 draft default tip

planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 81dd1e732f7264affc7b8acdf5ba174dbc0c32a9

1 <tool id="interactive_tool_chat_analysis" tool_type="interactive" name="Chat with your data" version="0.2">
2     <requirements>
3         <container type="docker">
4             quay.io/goeckslab/chatanalysis:smolagents
5         </container>
6     </requirements>
7     <entry_points>
8         <entry_point name="Chat with $input_dataset.element_identifier" requires_domain="True">
9             <port>
10                 8501
11             </port>
12             <url>
13                 /
14             </url>
15         </entry_point>
16     </entry_points>
17     <command>
18         <![CDATA[
19         echo "Starting Streamlit" &&
20         echo "working dir now: `pwd`" &&
21         mkdir -p generate_files &&
22         echo "input dataset: $input_dataset" &&
23         echo "input dataset datatype: $dataset_type" &&
24         ln -sf $__tool_directory__/.env /ChatAnalysis/.env &&
25         streamlit run /ChatAnalysis/smolagents_da.py
26             "$__user_email__"
27             "$openai_api_key_file"
28             "$groq_api_key_file"
29             "$chat_history"
30             "./generate_files"
31             "$input_dataset"
32             "$dataset_type"
33         ]]>
34     </command>
35     <configfiles>
36         <configfile name="openai_api_key_file"><![CDATA[
37             $__user__.extra_preferences.get('chatgpt|api_key')
38         ]]></configfile>
39         <configfile name="groq_api_key_file"><![CDATA[
40             $__user__.extra_preferences.get('groq|api_key')
41             ]]>
42         </configfile>
43     </configfiles>
44     <stdio>
45         <exit_code range="0:0" level="log"/>
46     </stdio>
47     <inputs>
48         <param name="input_dataset"  type="data" format="csv,tsv,h5ad,xlsx,xls,json,parquet,h5,fa,fasta,vcf,gtf,gff,bed" label="Data you want to chat with" optional="false"/>
49         <param name="dataset_type" type="select" label="The type of your dataset" >
50             <option value="csv">csv</option>
51             <option value="tsv">tsv</option>
52             <option value="h5ad">h5ad</option>
53             <option value="xlsx">xlsx</option>
54             <option value="xls">xls</option>
55             <option value="json">json</option>
56             <option value="parquet">parquet</option>
57             <option value="h5">h5</option>
58             <option value="fa">fa</option>
59             <option value="fasta">fasta</option>
60             <option value="vcf">vcf</option>
61             <option value="gtf">gtf</option>
62             <option value="gff">gff</option>
63             <option value="bed">bed</option>
64         </param>  
65     </inputs>
66     <outputs>
67         <data name="chat_history" format="json" label="${tool.name} -- chat history json on ${on_string} -- use to restore chat history next time"/>
68         <collection name="generate_files" type="list" label="${tool.name} -- generated files">
69             <discover_datasets pattern="__name_and_ext__" directory="generate_files" />
70         </collection>
71     </outputs>
72     <tests>
73         <test>
74         </test>
75     </tests>
76     <help>
77         Analyze and visualize a dataset with a Chat Agent.
78 
79         Start a ChatAnalysis instance after selecting a dataset — we provide free access to some LLMs.
80 
81         You are encouraged to use your own API keys, as the provided free access has limits. You can obtain a **free API key** for BambooLLM by signing up at https://pandas-ai.com and a **free API key** for Groq by signing up at https://groq.com.
82 
83         If you wish to set the OpenAI API key beforehand, go to **User → Preferences → Manage Information → ChatGPT → OpenAI API Key**. This way, you won’t need to set the OpenAI API key each time you use the app.
84 
85         Similarly, to set the Groq API key beforehand, navigate to **User → Preferences → Manage Information → Groq → API Key**.
86 
87         Alternatively, you can set the API key directly in the ChatAnalysis instance after it has started.
88     </help>
89 </tool>
90 
91