bwameth DM: fix test and modernize (#7799)

* fix test

* simplify test

* remove python wrapper

* bump:wq

* adaptto new schema

Author: bernt-matthias

data_managers/data_manager_bwameth_index_builder/data_manager/bwameth_index_builder.py

@@ -1,4 +1,4 @@
-<tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0.2" profile="18.09">
+<tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0.3" profile="24.2">
     <description>builder</description>
     <macros>
         <token name="@TOOL_VERSION@">0.2.2</token>
@@ -7,24 +7,35 @@
         <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
-#if str($sequence_id).strip():
-    #set $dbkey = $sequence_id
-#else:
-    #set $dbkey = $all_fasta_source.fields.dbkey
-#end if
-
-#if str($sequence_name).strip():
-    #set $name = $sequence_name
-#else:
-    #set $name = $all_fasta_source.fields.name
-#end if
-
-python '$__tool_directory__/bwameth_index_builder.py' --output '${out_file}'
---fasta_filename '${all_fasta_source.fields.path}'
---dbkey '${dbkey}'
---name '${name}'
---data_table_name bwameth_indexes
+        #import os.path
+        #set basename=os.path.basename($all_fasta_source.fields.path)
+        #set sym_linked_fasta_filename = os.path.join($out_file.extra_files_path, $basename)
+        mkdir -p '$out_file.extra_files_path' &&
+        ln -s '${all_fasta_source.fields.path}' '$sym_linked_fasta_filename' &&
+        bwameth.py index '$sym_linked_fasta_filename' &&
+        cp '$dmjson' '$out_file'
     ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[#slurp
+#import os.path
+#set basename=os.path.basename($all_fasta_source.fields.path)
+#set sym_linked_fasta_filename = os.path.join($out_file.extra_files_path, $basename)
+#set $value = $sequence_id or $all_fasta_source.fields.dbkey
+#set $name = $sequence_name or $all_fasta_source.fields.name
+{
+  "data_tables":{
+    "bwameth_indexes":[
+      {
+        "value": "${value}",
+        "dbkey": "${all_fasta_source.fields.dbkey}",
+        "name": "${name}",
+        "path": "$basename"
+      }
+    ]
+  }
+}
+]]></configfile>
+    </configfiles>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta" />
@@ -38,7 +49,14 @@ python '$__tool_directory__/bwameth_index_builder.py' --output '${out_file}'
     <tests>
         <test>
             <param name="all_fasta_source" value="phiX174"/>
-            <output name="out_file" value="bwameth_data_manager.json" compare="re_match"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="bwameth_indexes"/>
+                    <has_json_property_with_text property="dbkey" text="phiX174"/>
+                    <has_json_property_with_text property="name" text="phiX 174"/>
+                    <has_json_property_with_text property="value" text="phiX174"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[

data_managers/data_manager_bwameth_index_builder/data_manager/bwameth_index_builder.xml

@@ -8,9 +8,9 @@
                 <column name="name" />
                 <column name="path" output_ref="out_file" >
                     <move type="directory" relativize_symlinks="True">
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/bwameth_index/${value}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/bwameth_index/${value}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bwameth_index/${value}/${path}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bwameth_index/${value}/${path}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>