changeset 5:569f6683ef2d draft default tip

planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit a6103a83156aec5d739cae71b0507c5774731bb2

--- a/chat_analysis.xml	Tue Mar 25 16:02:25 2025 +0000
+++ b/chat_analysis.xml	Mon May 12 15:30:03 2025 +0000
@@ -1,7 +1,7 @@
-<tool id="interactive_tool_chat_analysis" tool_type="interactive" name="Chat with your data" version="0.2">
+<tool id="interactive_tool_chat_analysis" tool_type="interactive" name="Chat with your data" version="0.2.1">
     <requirements>
         <container type="docker">
-            quay.io/goeckslab/chatanalysis:smolagents
+            quay.io/goeckslab/chatanalysis:release
         </container>
     </requirements>
     <entry_points>
@@ -16,20 +16,28 @@
     </entry_points>
     <command>
         <![CDATA[
+        #import re
         echo "Starting Streamlit" &&
         echo "working dir now: `pwd`" &&
-        mkdir -p generate_files &&
+        mkdir -p generated_files &&
+        #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 datatype: $dataset_type" &&
+        echo "$input_dataset.ext" &&
         ln -sf $__tool_directory__/.env /ChatAnalysis/.env &&
-        streamlit run /ChatAnalysis/smolagents_da.py
+        streamlit run /ChatAnalysis/Chat.py
             "$__user_email__"
             "$openai_api_key_file"
             "$groq_api_key_file"
             "$chat_history"
-            "./generate_files"
+            "./generated_files"
             "$input_dataset"
-            "$dataset_type"
+            "$input_dataset.ext" 
+            --browser.gatherUsageStats false &&
+        echo "Streamlit finished" &&
+        echo "working dir now: '.' "
+
         ]]>
     </command>
     <configfiles>
@@ -46,27 +54,11 @@
     </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"/>
-        <param name="dataset_type" type="select" label="The type of your dataset" >
-            <option value="csv">csv</option>
-            <option value="tsv">tsv</option>
-            <option value="h5ad">h5ad</option>
-            <option value="xlsx">xlsx</option>
-            <option value="xls">xls</option>
-            <option value="json">json</option>
-            <option value="parquet">parquet</option>
-            <option value="h5">h5</option>
-            <option value="fa">fa</option>
-            <option value="fasta">fasta</option>
-            <option value="vcf">vcf</option>
-            <option value="gtf">gtf</option>
-            <option value="gff">gff</option>
-            <option value="bed">bed</option>
-        </param>  
     </inputs>
     <outputs>
         <data name="chat_history" format="json" label="${tool.name} -- chat history json on ${on_string} -- use to restore chat history next time"/>
-        <collection name="generate_files" type="list" label="${tool.name} -- generated files">
-            <discover_datasets pattern="__name_and_ext__" directory="generate_files" />
+        <collection name="generated_files" type="list" label="${tool.name} -- generated files">
+            <discover_datasets pattern="__name_and_ext__" directory="generated_files" />
         </collection>
     </outputs>
     <tests>