Mercurial > repos > goeckslab > chatanalysis

annotate chat_analysis.xml @ 8:13cf52df8751 draft

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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit d5abc2e6d0f950fbc883bde2f153c47b87bd7f8c
author goeckslab
date Fri, 20 Jun 2025 17:57:10 +0000
parents ea1c4179b2b9
children ebff1089e004
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1 <tool id="interactive_tool_chat_analysis" tool_type="interactive" name="Data Analysis Agent" version="0.3.0">
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2 <icon src="datachat.png" />
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3 <description>Interactively chats using natural language to explore, visualize, and analyze your data</description>
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4 <requirements>
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5 <container type="docker">
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6 quay.io/goeckslab/chatanalysis:0.3.0
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7 </container>
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8 </requirements>
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9 <entry_points>
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10 <entry_point name="Chat with $input_dataset.element_identifier" requires_domain="True">
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11 <port>
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12 9090
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13 </port>
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14 <url>
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15 /
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16 </url>
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17 </entry_point>
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18 </entry_points>
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19 <command>
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20 <![CDATA[
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21 #import re
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22 echo "Starting Streamlit" &&
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23 echo "working dir now: `pwd`" &&
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24 mkdir -p outputs_dir &&
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25 #set $sanitized_input_dataset = re.sub('[^\w\-_\.]', '_', $input_dataset.element_identifier.strip())
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26 ln -sf '$input_dataset' "./${sanitized_input_dataset}";
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27 echo "sanitized input dataset: $sanitized_input_dataset" &&
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28 echo "input dataset: $input_dataset" &&
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29 echo "$input_dataset.ext" &&
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30 ln -sf $__tool_directory__/.env /ChatAnalysis/.env &&
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31 python /ChatAnalysis/chat_dspy.py
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32 --user_id "$__user_email__"
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33 --openai_key_file "$openai_api_key_file"
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34 --groq_key_file "$groq_api_key_file"
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35 --chat_history "$chat_history"
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36 --outputs_dir "./outputs_dir"
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37 --input_file "$input_dataset"
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38 --input_type "$input_dataset.ext" &&
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39 echo "finished" &&
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40 echo "working dir now: '.' "
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41
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42 ]]>
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43 </command>
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44 <configfiles>
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45 <configfile name="openai_api_key_file"><![CDATA[
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46 $__user__.extra_preferences.get('chatgpt|api_key')
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47 ]]></configfile>
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48 <configfile name="groq_api_key_file"><![CDATA[
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49 $__user__.extra_preferences.get('groq|api_key')
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50 ]]>
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51 </configfile>
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52 </configfiles>
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53 <stdio>
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54 <exit_code range="0:0" level="log"/>
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55 </stdio>
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56 <inputs>
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57 <param name="input_dataset" type="data" format="csv,tsv,h5ad,xlsx,xls,json,parquet,h5,fa,fasta,vcf,gtf,gff,bed" label="Data you want to chat with" optional="false"/>
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58 </inputs>
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59 <outputs>
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60 <data name="chat_history" format="json" label="${tool.name} -- chat history json on ${on_string} -- use to restore chat history next time"/>
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61 <collection name="generated_files" type="list" label="${tool.name} -- generated files">
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62 <discover_datasets pattern="__name_and_ext__" directory="generated_files" />
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63 </collection>
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64 </outputs>
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65 <tests>
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66 <test>
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67 </test>
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68 </tests>
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69 <help>
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70 Analyze and visualize a dataset with a Chat Agent.
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71
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72 Start a ChatAnalysis instance after selecting a dataset — we provide free access to some LLMs.
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74 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.
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76 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.
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77
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78 Similarly, to set the Groq API key beforehand, navigate to **User → Preferences → Manage Information → Groq → API Key**.
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79
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80 Alternatively, you can set the API key directly in the ChatAnalysis instance after it has started.
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81 </help>
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82 </tool>