comparison chat_analysis.xml @ 10:e8cdf238cc02 draft

planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 24ca42c53d1206fe9cd5e15fc63da9ba54b2a230

9:ebff1089e004

        echo "Starting Streamlit" &&
        echo "working dir now: `pwd`" &&
        mkdir -p outputs_dir &&
        #set $sanitized_input_dataset = re.sub('[^\w\-_\.]', '_', $input_dataset.element_identifier.strip())
        ln -sf '$input_dataset' "./${sanitized_input_dataset}";
        echo "sanitized input dataset: $sanitized_input_dataset" &&
        echo "input dataset: $input_dataset" &&
        echo "$input_dataset.ext" &&
        ln -sf $__tool_directory__/.env /ChatAnalysis/.env &&
        python /ChatAnalysis/chat_dspy.py
            --user_id "$__user_email__"
            --openai_key_file "$openai_api_key_file"
            --groq_key_file "$groq_api_key_file"
            --chat_history "$chat_history"
            --outputs_dir "./outputs_dir"
            --input_file "$input_dataset"
            --input_type "$input_dataset.ext" &&
        echo "finished" &&
        echo "working dir now: '.' "

        ]]>
    </command>

    </configfiles>
    <stdio>
        <exit_code range="0:0" level="log"/>
    </stdio>
    <inputs>
        <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"/>
    </inputs>
    <outputs>
        <data name="chat_history" format="json" label="${tool.name} -- chat history json on ${on_string} -- use to restore chat history next time"/>
        <collection name="generated_files" type="list" label="${tool.name} -- generated files">
            <discover_datasets pattern="__name_and_ext__" directory="generated_files" />

10:e8cdf238cc02

        echo "Starting Streamlit" &&
        echo "working dir now: `pwd`" &&
        mkdir -p outputs_dir &&
        #set $sanitized_input_dataset = re.sub('[^\w\-_\.]', '_', $input_dataset.element_identifier.strip())
        ln -sf '$input_dataset' "./${sanitized_input_dataset}";
        ln -sf '$input_dataset' "outputs_dir/${sanitized_input_dataset}"; 
        echo "sanitized input dataset: $sanitized_input_dataset" &&
        echo "input dataset: $input_dataset" &&
        echo "$input_dataset.ext" &&
        python /ChatAnalysis/dspy_agent/chat_dspy.py
            --user_id "$__user_name__"
            --openai_key_file "$openai_api_key_file"
            --groq_key_file "$groq_api_key_file"
            --chat_history "$chat_history"
            --outputs_dir "./outputs_dir"
            --input_file "$input_dataset"
            --input_type "$input_dataset.ext"
            --file_name "${sanitized_input_dataset}" &&
        echo "finished" &&
        echo "working dir now: '.' "

        ]]>
    </command>

    </configfiles>
    <stdio>
        <exit_code range="0:0" level="log"/>
    </stdio>
    <inputs>
        <param name="input_dataset"  type="data" format="csv,tsv,h5ad,xlsx,xls" label="Data you want to chat with" optional="false"/>
    </inputs>
    <outputs>
        <data name="chat_history" format="json" label="${tool.name} -- chat history json on ${on_string} -- use to restore chat history next time"/>
        <collection name="generated_files" type="list" label="${tool.name} -- generated files">
            <discover_datasets pattern="__name_and_ext__" directory="generated_files" />