# HG changeset patch
# User iuc
# Date 1733381232 0
# Node ID a96a36c08c5be4aafc2c9b67069791088f2a5942
# Parent  dfc6651714920aeaea52f4a33860910ac0e8a616
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219

diff -r dfc665171492 -r a96a36c08c5b data_manager/bwa_mem2_index_builder.xml
--- a/data_manager/bwa_mem2_index_builder.xml	Mon Sep 30 10:12:25 2024 +0000
+++ b/data_manager/bwa_mem2_index_builder.xml	Thu Dec 05 06:47:12 2024 +0000
@@ -1,8 +1,8 @@
-<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">
+<tool id="bwa_mem2_index_builder_data_manager" name="BWA-MEM2 index builder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="23.0">
     <description></description>
     <macros>
         <token name="@TOOL_VERSION@">2.2.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bwa-mem2</requirement>
@@ -52,7 +52,7 @@
         <test>
             <param name="all_fasta_source" value="phiX174"/>
             <param name="sequence_name" value="Galeocerdo cuvier"/>
-            <param name="sequence_id" value="fooBar1"/>
+            <param name="sequence_id" value="tigHai1"/>
             <output name="out_file" file="bwa_mem2_data_manager.2.json"/>
         </test>
     </tests>
diff -r dfc665171492 -r a96a36c08c5b data_manager_conf.xml
--- a/data_manager_conf.xml	Mon Sep 30 10:12:25 2024 +0000
+++ b/data_manager_conf.xml	Thu Dec 05 06:47:12 2024 +0000
@@ -9,9 +9,9 @@
                 <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}">${dbkey}/bwa_mem2_index/${value}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/bwa_mem_index/v2/${value}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bwa_mem2_index/${value}/${path}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bwa_mem_index/v2/${value}/${path}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
diff -r dfc665171492 -r a96a36c08c5b test-data/all_fasta.loc
--- a/test-data/all_fasta.loc	Mon Sep 30 10:12:25 2024 +0000
+++ b/test-data/all_fasta.loc	Thu Dec 05 06:47:12 2024 +0000
@@ -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
diff -r dfc665171492 -r a96a36c08c5b test-data/bwa_mem2_data_manager.1.json
--- a/test-data/bwa_mem2_data_manager.1.json	Mon Sep 30 10:12:25 2024 +0000
+++ b/test-data/bwa_mem2_data_manager.1.json	Thu Dec 05 06:47:12 2024 +0000
@@ -4,7 +4,7 @@
       {
         "value": "phiX174",
         "dbkey": "phiX174",
-        "name": "phiX174",
+        "name": "phiX 174",
         "path": "phiX174.fasta"
       }
     ]
diff -r dfc665171492 -r a96a36c08c5b test-data/bwa_mem2_data_manager.2.json
--- a/test-data/bwa_mem2_data_manager.2.json	Mon Sep 30 10:12:25 2024 +0000
+++ b/test-data/bwa_mem2_data_manager.2.json	Thu Dec 05 06:47:12 2024 +0000
@@ -2,7 +2,7 @@
   "data_tables":{
     "bwa_mem2_indexes":[
       {
-        "value": "fooBar1",
+        "value": "tigHai1",
         "dbkey": "phiX174",
         "name": "Galeocerdo cuvier",
         "path": "phiX174.fasta"