Mercurial > repos > goeckslab > chatanalysis
annotate chat_analysis.xml @ 7:ea1c4179b2b9 draft
planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
author | goeckslab |
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date | Sat, 14 Jun 2025 02:45:41 +0000 |
parents | 1ee654186809 |
children | 13cf52df8751 |
rev | line source |
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7
ea1c4179b2b9
planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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1 <tool id="interactive_tool_chat_analysis" tool_type="interactive" name="Chat with your data" version="0.3.0"> |
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2 <icon src="datachat.png" /> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 8da37a699458454bcb1ce336754404206485b0ff
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3 <description>Use natural language to work with and analyze your data</description> |
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4 <requirements> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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5 <container type="docker"> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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6 quay.io/goeckslab/chatanalysis:0.3.0 |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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7 </container> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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8 </requirements> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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9 <entry_points> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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10 <entry_point name="Chat with $input_dataset.element_identifier" requires_domain="True"> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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11 <port> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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12 9090 |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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13 </port> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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14 <url> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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15 / |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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16 </url> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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17 </entry_point> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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18 </entry_points> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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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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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit f4ecf0087e42199a991ed4d9556e16cefdb7d4cb
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23 echo "working dir now: `pwd`" && |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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24 mkdir -p outputs_dir && |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit a6103a83156aec5d739cae71b0507c5774731bb2
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25 #set $sanitized_input_dataset = re.sub('[^\w\-_\.]', '_', $input_dataset.element_identifier.strip()) |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit a6103a83156aec5d739cae71b0507c5774731bb2
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26 ln -sf '$input_dataset' "./${sanitized_input_dataset}"; |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit a6103a83156aec5d739cae71b0507c5774731bb2
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27 echo "sanitized input dataset: $sanitized_input_dataset" && |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 81dd1e732f7264affc7b8acdf5ba174dbc0c32a9
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28 echo "input dataset: $input_dataset" && |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit a6103a83156aec5d739cae71b0507c5774731bb2
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29 echo "$input_dataset.ext" && |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 81dd1e732f7264affc7b8acdf5ba174dbc0c32a9
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30 ln -sf $__tool_directory__/.env /ChatAnalysis/.env && |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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31 python /ChatAnalysis/chat_dspy.py |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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32 --user_id "$__user_email__" |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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33 --openai_key_file "$openai_api_key_file" |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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34 --groq_key_file "$groq_api_key_file" |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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35 --chat_history "$chat_history" |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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36 --outputs_dir "./outputs_dir" |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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37 --input_file "$input_dataset" |
ea1c4179b2b9
planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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38 --input_type "$input_dataset.ext" && |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit ca6d6493b0ebe9daa65de5ff5ea13b3e412c86c3
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39 echo "finished" && |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit a6103a83156aec5d739cae71b0507c5774731bb2
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40 echo "working dir now: '.' " |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit a6103a83156aec5d739cae71b0507c5774731bb2
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41 |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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42 ]]> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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43 </command> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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44 <configfiles> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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45 <configfile name="openai_api_key_file"><![CDATA[ |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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46 $__user__.extra_preferences.get('chatgpt|api_key') |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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47 ]]></configfile> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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48 <configfile name="groq_api_key_file"><![CDATA[ |
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49 $__user__.extra_preferences.get('groq|api_key') |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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50 ]]> |
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51 </configfile> |
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52 </configfiles> |
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53 <stdio> |
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54 <exit_code range="0:0" level="log"/> |
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55 </stdio> |
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56 <inputs> |
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57 <param name="input_dataset" type="data" format="csv,tsv,h5ad,xlsx,xls,json,parquet,h5,fa,fasta,vcf,gtf,gff,bed" label="Data you want to chat with" optional="false"/> |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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58 </inputs> |
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59 <outputs> |
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60 <data name="chat_history" format="json" label="${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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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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72 Start a ChatAnalysis instance after selecting a dataset — we provide free access to some LLMs. |
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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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73 |
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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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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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75 |
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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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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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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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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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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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planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 2d72b2974a22a70ca07ed81baaa01e9ade8c1acc
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81 </help> |
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82 </tool> |