Update logan search_proteins to 2.10.1

Author: SaimMomin12

tools/logan_proteins/macros.xml

@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.2.2</token>
+    <token name="@TOOL_VERSION@">2.10.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">25.0</token>
     <xml name="requirements">
         <requirements>
-            <container type="docker">quay.io/bgruening/logan-protein:1.2.2</container>
+            <container type="docker">quay.io/bgruening/logan-protein:@TOOL_VERSION@</container>
         </requirements>
     </xml>
     <xml name="citations">

tools/logan_proteins/search_database.xml

@@ -5,26 +5,37 @@
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
+        if [ -n "\$GALAXY_LOGAN_PROTEIN_SEARCH_FORCE_CPU" ]; then
+            FORCE_CPU="--force_cpu";
+        else
+            FORCE_CPU="";
+        fi &&
         mkdir results &&
         mkdir -p results/intermediate_files &&       
         ln -s '$query_embeddings_npy' results/intermediate_files/query_embeddings.npy &&
         ln -s '$query_embeddings_names' results/intermediate_files/query_embeddings.names.txt &&
         ln -s '$query_sequences' query_sequences.fasta &&
         python /app/search_database.py
             --database '$database.fields.path'
+            --db-type '$database_type'
             $deep_search
             --output results/
             --query_sequences query_sequences.fasta
-            --num_threads \${GALAXY_SLOTS:-8}
-            --memory \${GALAXY_MEMORY_MB:-16000}
+            --num_threads "\${GALAXY_SLOTS:-8}"
+            --memory "\${GALAXY_MEMORY_MB:-16000}"
             #if $outfmt:
                 --outfmt '$outfmt'
             #end if
+            \$FORCE_CPU
     ]]></command>
     <inputs>
         <param name="query_sequences" type="data" format="fasta" label="Original query sequences (FASTA)" help="Same FASTA file used in the embedding step, needed for MMseqs2 alignment" />
         <param name="query_embeddings_npy" type="data" format="npy" label="Query embeddings (npy)" help="Output from the Embed Query tool" />
         <param name="query_embeddings_names" type="data" format="txt" label="Query embedding names" help="Output from the Embed Query tool" />
+        <param name="database_type" type="select" label="Database Type" help="Select the database type">
+            <option value="faiss" selected="true">FAISS</option>
+            <option value="usearch">usearch</option>
+        </param>
         <param name="database" type="select" label="FAISS Database" help="Select FAISS database">
             <options from_data_table="faiss_protein_databases">
                 <filter type="sort_by" column="3"/>
@@ -43,6 +54,7 @@
     </inputs>
 
     <outputs>
+        <data name="diversified_hits" from_work_dir="results/diversified_hits.tsv" format="tsv" label="${tool.name} on ${on_string}: Diversified hits (TSV)"/>
         <data name="matches_fasta" from_work_dir="results/matches.fasta" format="fasta" label="${tool.name} on ${on_string}: Matched proteins (FASTA)"/>
         <data name="matches_mmseqs2" from_work_dir="results/matches.mmseqs2" format="tabular" label="${tool.name} on ${on_string}: MMseqs2 alignments"/>
         <data name="all_results" from_work_dir="results/intermediate_files/all_results.fasta" format="fasta" label="${tool.name} on ${on_string}: All similar proteins (FASTA)"/>

tools/logan_proteins/test-data/faiss_database.loc

@@ -3,4 +3,5 @@
 # - db-name
 # - version
 # - /path/to/data 
-faiss-demo-db-20260203	FAISS Test Database	1.2.2	${__HERE__}/test-db/
+faiss-demo-db-20260203	FAISS Test Database	1.2.2	${__HERE__}/test-db/
+faiss-demo-db-20260203	FAISS Test Database	2.10.1	${__HERE__}/test-db/

tools/logan_proteins/test-data/test-db/centroids.fa

@@ -0,0 +1,4 @@
+>centroid_0
+MKTAYIAKQR
+>centroid_1
+MSEQNNTEMT