--- a/data_manager/bowtie_index_builder.xml	Sun Apr 16 08:26:06 2023 +0000
+++ b/data_manager/bowtie_index_builder.xml	Thu Dec 05 06:47:05 2024 +0000
@@ -1,16 +1,39 @@
-<tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="1.2.0">
+<tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>builder</description>
+    <macros>
+        <token name="@WRAPPER_VERSION@">1.3.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.2.0">bowtie</requirement>
+        <requirement type="package" version="@WRAPPER_VERSION@">bowtie</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-python '$__tool_directory__/bowtie_index_builder.py'
-'${out_file}'
---fasta_filename '${all_fasta_source.fields.path}'
---fasta_dbkey '${all_fasta_source.fields.dbkey}'
---fasta_description '${all_fasta_source.fields.name}'
---data_table_name bowtie_indexes
-    ]]></command>
+        #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
+        mkdir -p '${out_file.extra_files_path}' &&
+        ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
+        bowtie-build '${out_file.extra_files_path}/${fasta_file_name}' '${out_file.extra_files_path}/${fasta_file_name}' &&
+        cp '$dmjson' '$out_file'
+        ]]>
+    </command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[#slurp
+#set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
+#set $value = $sequence_id or $all_fasta_source.fields.dbkey
+#set $name = $sequence_name or $all_fasta_source.fields.name
+{
+  "data_tables":{
+    "bowtie_indexes":[
+      {
+        "value": "${value}",
+        "dbkey": "${all_fasta_source.fields.dbkey}",
+        "name": "${name}",
+        "path": "${fasta_file_name}"
+      }
+    ]
+  }
+}
+]]></configfile>
+    </configfiles>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta"/>
@@ -21,6 +44,18 @@
     <outputs>
         <data name="out_file" format="data_manager_json"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <output name="out_file" file="bowtie_data_manager.1.json"/>
+        </test>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <param name="sequence_name" value="Galeocerdo cuvier"/>
+            <param name="sequence_id" value="tigHai1"/>
+            <output name="out_file" file="bowtie_data_manager.2.json"/>
+        </test>
+    </tests>
     <help><![CDATA[
 .. class:: infomark