Drop python wrapper

data_managers/data_manager_bwa_mem2_index_builder/data_manager/bwa_mem2_index_builder.xml

@@ -1,18 +1,39 @@
-<tool id="bwa_mem2_index_builder_data_manager" name="BWA-MEM2 index" tool_type="manage_data" version="0.0.1" profile="19.05">
-    <description>builder</description>
+<tool id="bwa_mem2_index_builder_data_manager" name="Build BWA-MEM2 indexes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05">
+    <description></description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.2.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="2.2.1">bwa-mem2</requirement>
-        <requirement type="package" version="3.9">python</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bwa-mem2</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/bwa_mem2_index_builder.py'
-        --output '${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 bwa_mem2_indexes
+        #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}' &&
+        bwa-mem2 index '${out_file.extra_files_path}/${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 $all_fasta_source.fields.name
+{
+  "data_tables":{
+    "bwa_mem2_indexes":[
+      {
+        "value": "${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"/>
@@ -26,7 +47,13 @@
     <tests>
         <test>
             <param name="all_fasta_source" value="phiX174"/>
-            <output name="out_file" file="bwa_mem2_data_manager.json"/>
+            <output name="out_file" file="bwa_mem2_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="fooBar1"/>
+            <output name="out_file" file="bwa_mem2_data_manager.2.json"/>
         </test>
     </tests>
     <help>

data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.1.json

@@ -0,0 +1,12 @@
+{
+  "data_tables":{
+    "bwa_mem2_indexes":[
+      {
+        "value": "phiX174",
+        "dbkey": "phiX174",
+        "name": "phiX174",
+        "path": "phiX174.fasta"
+      }
+    ]
+  }
+}

data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.2.json

@@ -0,0 +1,12 @@
+{
+  "data_tables":{
+    "bwa_mem2_indexes":[
+      {
+        "value": "fooBar1",
+        "dbkey": "phiX174",
+        "name": "Galeocerdo cuvier",
+        "path": "phiX174.fasta"
+      }
+    ]
+  }
+}