Update data_manager_sam_fasta_index_builder for normalized layout, plus:

- Drop python wrapper
- Update samtools version
- Add test of non-default options

data_managers/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.xml

@@ -1,17 +1,39 @@
-<tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.6" profile="19.05">
+<tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>builder</description>
+    <macros>
+        <token name="@WRAPPER_VERSION@">1.21</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.14">samtools</requirement>
-        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="1.21">samtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/data_manager_sam_fasta_index_builder.py'
-        '${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 fasta_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}' &&
+        cd '${out_file.extra_files_path}' &&
+        samtools faidx '${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 $all_fasta_source.fields.name
+{
+  "data_tables":{
+    "fasta_indexes":[
+      {
+        "value": "${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"/>
@@ -25,7 +47,13 @@
     <tests>
         <test>
             <param name="all_fasta_source" value="phiX174"/>
-            <output name="out_file" value="sam_fasta_data_manager.json"/>
+            <output name="out_file" value="sam_fasta_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" value="sam_fasta_data_manager.2.json"/>
         </test>
     </tests>
 

data_managers/data_manager_sam_fasta_index_builder/data_manager_conf.xml

@@ -1,6 +1,5 @@
 <?xml version="1.0"?>
 <data_managers>
-
     <data_manager tool_file="data_manager/data_manager_sam_fasta_index_builder.xml" id="sam_fasta_index_builder">
         <data_table name="fasta_indexes">
             <output>
@@ -10,13 +9,12 @@
                 <column name="path" output_ref="out_file" >
                     <move type="directory" relativize_symlinks="True">
                         <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/sam_indexes/${value}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/sam_fasta_index/v1/${value}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/sam_indexes/${value}/${path}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/sam_fasta_index/v1/${value}/${path}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
         </data_table>
     </data_manager>
-
 </data_managers>

data_managers/data_manager_sam_fasta_index_builder/test-data/all_fasta.loc

@@ -16,4 +16,4 @@
 #fasta file. So there will be multiple fasta files for each build,
 #such as with hg19 above.
 #
-phiX174	phiX174	phiX174	${__HERE__}/phiX174.fasta
+phiX174	phiX174	phiX 174	${__HERE__}/phiX174.fasta

data_managers/data_manager_sam_fasta_index_builder/test-data/sam_fasta_data_manager.1.json

@@ -0,0 +1,12 @@
+{
+  "data_tables":{
+    "fasta_indexes":[
+      {
+        "value": "phiX174",
+        "dbkey": "phiX174",
+        "name": "phiX 174",
+        "path": "phiX174.fasta"
+      }
+    ]
+  }
+}

data_managers/data_manager_sam_fasta_index_builder/test-data/sam_fasta_data_manager.2.json

@@ -0,0 +1,12 @@
+{
+  "data_tables":{
+    "fasta_indexes":[
+      {
+        "value": "tigHai1",
+        "dbkey": "phiX174",
+        "name": "Galeocerdo cuvier",
+        "path": "phiX174.fasta"
+      }
+    ]
+  }
+}

data_managers/data_manager_sam_fasta_index_builder/tool_data_table_conf.xml.sample

@@ -1,10 +1,10 @@
-<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
 <tables>
     <!-- Locations of all fasta files under genome directory -->
     <table name="all_fasta" comment_char="#">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/all_fasta.loc" />
     </table>
+    <!-- Locations of fasta indexes generated by samtools faidx -->
     <table name="fasta_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/fasta_indexes.loc" />