# HG changeset patch
# User goeckslab
# Date 1750483415 0
# Node ID e8cdf238cc0277a1d44df73eb3fbe086b443f934
# Parent  ebff1089e0048627b43a1e6b57588896d9b3d2d5
planemo upload for repository https://github.com/goeckslab/ChatAnalysis commit 24ca42c53d1206fe9cd5e15fc63da9ba54b2a230

diff -r ebff1089e004 -r e8cdf238cc02 chat_analysis.xml
--- a/chat_analysis.xml	Fri Jun 20 18:46:25 2025 +0000
+++ b/chat_analysis.xml	Sat Jun 21 05:23:35 2025 +0000
@@ -24,18 +24,19 @@
         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" &&
-        ln -sf $__tool_directory__/.env /ChatAnalysis/.env &&
-        python /ChatAnalysis/chat_dspy.py
-            --user_id "$__user_email__"
+        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" &&
+            --input_type "$input_dataset.ext"
+            --file_name "${sanitized_input_dataset}" &&
         echo "finished" &&
         echo "working dir now: '.' "
 
@@ -54,7 +55,7 @@
         <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"/>
+        <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"/>