remove filtertaxseqdb conditionnal

tools/mmseqs2/mmseqs2_taxonomy_assignment.xml

@@ -16,9 +16,9 @@ mmseqs createdb
     --dbtype '$createdb.dbtype'
     --createdb-mode $createdb.createdb_mode
     --shuffle $createdb.shuffle &&
-ls -lah '$createtaxdb.database_type.mmseqs2_db_select.fields.path' &&
+
 cp -r '$createtaxdb.database_type.mmseqs2_db_select.fields.path'/database* . &&
-ls -lah &&
+
 mmseqs createtaxdb
     database
     'tmp'
@@ -27,22 +27,21 @@ mmseqs createtaxdb
     #end if
     --tax-mapping-mode '$createtaxdb.tax_mapping_mode'
     --threads "\${GALAXY_SLOTS:-1}" &&
-    #if str($filtertaxseqdb.filtertaxseqdb_bool.use_filter) == "yes"
+    #if $filtertaxseqdb.taxon_list
         mmseqs filtertaxseqdb
-            'sequenceDB'
-            'sequenceDB_filtered' &&
-            #if str($filtertaxseqdb.filtertaxseqdb_bool.use_filter.taxon_list) != ""
-                --taxon-list '$filtertaxseqdb.filtertaxseqdb_bool.use_filter.taxon_list' &&
-            #end if
+            'database'
+            'database_filtered'
+            --taxon-list '$filtertaxseqdb.taxon_list'
+             &&
     #end if
-ls -lah &&
+
 mmseqs taxonomy
-    #if str($filtertaxseqdb.filtertaxseqdb_bool.use_filter) == "yes"
-        'sequenceDB_filtered'
+    'sequenceDB'
+    #if $filtertaxseqdb.taxon_list
+        'database_filtered'
     #else 
-        'sequenceDB'
+        'database'
     #end if
-    database
     'output_taxonomy'
     'tmp'
     #if str($taxonomy.alph_type.type) == "amino_acid"
@@ -174,11 +173,7 @@ mmseqs taxonomy
     ##--strand INT                     Strand selection only works for DNA/DNA search 0: reverse, 1: forward, 2: both [1]
 &&
 mmseqs createtsv
-    #if str($filtertaxseqdb.filtertaxseqdb_bool.use_filter) == "yes"
-        'sequenceDB_filtered'
-    #else 
-        'sequenceDB'
-    #end if
+    'sequenceDB'
     'output_taxonomy'
     'taxo_result.tsv'
 
@@ -194,7 +189,11 @@ mmseqs createtsv
 #if str($kraken_report.keep_report) == "Yes"
 &&
     mmseqs taxonomyreport
-        database
+    #if $filtertaxseqdb.taxon_list
+        'database_filtered'
+    #else 
+        'database'
+    #end if
         'output_taxonomy'
         'taxo_result.txt'
         --report-mode 0
@@ -203,7 +202,11 @@ mmseqs createtsv
 #if str($krona_report.keep_report) == "Yes"
 &&
     mmseqs taxonomyreport
-        database
+    #if $filtertaxseqdb.taxon_list
+        'database_filtered'
+    #else 
+        'database'
+    #end if
         'output_taxonomy'
         'taxo_result.html'
         --report-mode 1
@@ -266,16 +269,7 @@ mmseqs createtsv
             </param>
         </section>
         <section name="filtertaxseqdb" title="Filter taxonomy sequence database">
-            <conditional name="filtertaxseqdb_bool">
-                <param name="use_filter" type="select" label="Do you want to retain (or exclude) sequences based on their taxonomic labels?" help="" >
-                    <option value="no" selected="true">No</option>
-                    <option value="yes">Yes</option>
-                </param>
-                <when value="no"/>
-                <when value="yes">
-                    <param argument="--taxon-list" type="text" optional="true" value="" label="Taxonomy ID" help="Possibly multiple values separated by ','"/>
-                </when>
-            </conditional>
+            <param argument="--taxon-list" type="text" optional="true" value="" label="Taxonomy ID" help="Possibly multiple values separated by ','"/>
         </section>
         <section name="taxonomy" title="Taxonomy assignment by computing the lowest common ancestor of homologs">
             <conditional name="alph_type">
@@ -549,6 +543,9 @@ mmseqs createtsv
                     <param name="mmseqs2_db_select" value="UniProtKB/Swiss-Prot-15.6f452-15112024" />
                 </conditional>
             </section>
+            <section name="filtertaxseqdb">
+                <param name="taxon_list" value="2" />
+            </section>
             <conditional name="krona_report">
                 <param name="keep_report" value="No"/>
             </conditional>