diff cdhit_analysis.xml @ 2:706b7acdb230 draft

planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_clusters_tool commit c2020ecc91cea0c8cf7439180cf796743c838b4d-dirty

--- a/cdhit_analysis.xml	Mon Oct 20 12:27:31 2025 +0000
+++ b/cdhit_analysis.xml	Tue Oct 21 07:54:21 2025 +0000
@@ -9,7 +9,7 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/cdhit_analysis.py'
+bash '$__tool_directory__/cdhit_analysis.sh'
         --input_cluster '$input_cluster'
         --input_annotation '$input_annotation'
 
@@ -17,13 +17,16 @@
             --output_similarity_txt '$similarity_txt'
             --output_similarity_plot '$similarity_plot'
         #end if
+
         #if $output_options.evalue_output:
             --output_evalue_txt '$evalue_txt'
             --output_evalue_plot '$evalue_plot'
         #end if
+
         #if $output_options.count_output:
             --output_count '$cluster_count'
         #end if
+
         #if $output_options.taxa_output:
             --output_taxa_clusters '$cluster_taxa'
             --output_taxa_processed '$processed_taxa'
@@ -39,9 +42,11 @@
         #if $processing_options.show_unannotated_clusters:
             --show_unannotated_clusters
         #end if
+
         #if $processing_options.make_taxa_in_cluster_split:
             --make_taxa_in_cluster_split
         #end if
+
         #if $processing_options.print_empty_files:
             --print_empty_files
         #end if