eliminate cached_to_index option

bgruening · Oct 20, 2023 · 4c306ed · 4c306ed
1 parent 862987c
commit 4c306ed
Showing 1 changed file with 4 additions and 18 deletions.
diff --git a/tools/rna_tools/sortmerna/sortmerna.xml b/tools/rna_tools/sortmerna/sortmerna.xml
@@ -31,18 +31,14 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
     mkdir -p './aligned' &&
     mkdir -p './kvdb_folder' &&
     mkdir -p './readb_folder' &&
-    #if $databases_type.databases_selector != 'cached'
-        mkdir -p './idx_folder' &&
-    #end if
+    mkdir -p './idx_folder' &&
 
     sortmerna
         #for $reference in $ref
             --ref '$reference'
         #end for
-        #if $databases_type.databases_selector != 'cached'
-            -L '$databases_type.seed_length'
-            --max_pos '$databases_type.max_pos'
-        #end if
+        -L '$databases_type.seed_length'
+        --max_pos '$databases_type.max_pos'
         --aligned 'aligned'
         #if $sequencing_type.sequencing_type_selector == 'paired'
             --reads '$sequencing_type.forward_reads'
@@ -133,8 +129,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
         <conditional name="databases_type">
             <param name="databases_selector" type="select" label="Databases to query"
                 help="Public rRNA databases provided with SortMeRNA have been indexed. On the contrary, personal databases must be indexed each time SortMeRNA is launched. Please be patient, this may take some time depending on the size of the given database.">
-                <option value="cached" selected="true">Public pre-indexed ribosomal databases</option>
-                <option value="cached_to_index">Public ribosomal databases to index with non default parameters</option>
+                <option value="cached" selected="true">Public ribosomal databases</option>
                 <option value="history">Databases from your history</option>
             </param>
             <when value="cached">
@@ -145,15 +140,6 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
                     </options>
                     <validator type="no_options" message="No options available. Contact your Galaxy administrator."/>
                 </param>
-            </when>
-            <when value="cached_to_index">
-                <param name="input_databases" label="rRNA databases" type="select" optional="false" multiple="true">
-                    <options from_data_table="rRNA_databases">
-                        <column name="name" index="1"/>
-                        <column name="value" index="2"/>
-                    </options>
-                    <validator type="no_options" message="No options available. Contact your Galaxy administrator."/>
-                </param>
                 <expand macro="db_prep"/>
             </when>
             <when value="history">