# HG changeset patch
# User iuc
# Date 1733381238 0
# Node ID 74dbe9e6c888af33f2eaca86dd2fb90fc2b804fe
# Parent  0429479e3821c4db4dbfe03925a3fabe10ea9aef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219

diff -r 0429479e3821 -r 74dbe9e6c888 data_manager/bwa_mem_index_builder.py
--- a/data_manager/bwa_mem_index_builder.py	Sun Apr 16 08:27:00 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,102 +0,0 @@
-#!/usr/bin/env python
-# Dan Blankenberg
-from __future__ import print_function
-
-import json
-import optparse
-import os
-import subprocess
-import sys
-
-CHUNK_SIZE = 2**20
-TWO_GB = 2**30 * 2
-DEFAULT_DATA_TABLE_NAME = "bwa_mem_indexes"
-
-
-def get_id_name(params, dbkey, fasta_description=None):
-    # TODO: ensure sequence_id is unique and does not already appear in location file
-    sequence_id = params['param_dict']['sequence_id']
-    if not sequence_id:
-        sequence_id = dbkey
-
-    sequence_name = params['param_dict']['sequence_name']
-    if not sequence_name:
-        sequence_name = fasta_description
-        if not sequence_name:
-            sequence_name = dbkey
-    return sequence_id, sequence_name
-
-
-def build_bwa_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME):
-    # TODO: allow multiple FASTA input files
-    fasta_base_name = os.path.split(fasta_filename)[-1]
-    sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
-    os.symlink(fasta_filename, sym_linked_fasta_filename)
-    if params['param_dict']['index_algorithm'] == 'automatic':
-        if os.stat(fasta_filename).st_size < TWO_GB:  # use 2 GB as cut off for memory vs. max of 2gb database size; this is somewhat arbitrary
-            index_algorithm = 'is'
-        else:
-            index_algorithm = 'bwtsw'
-    else:
-        index_algorithm = params['param_dict']['index_algorithm']
-
-    args = ['bwa', 'index', '-a', index_algorithm]
-    args.append(sym_linked_fasta_filename)
-    proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
-    return_code = proc.wait()
-    if return_code:
-        print("Error building index.", file=sys.stderr)
-        sys.exit(return_code)
-    data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name)
-    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
-
-
-def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
-    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
-    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
-    data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
-    return data_manager_dict
-
-
-def main():
-    parser = optparse.OptionParser()
-    parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
-    parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
-    parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
-    parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name')
-    (options, args) = parser.parse_args()
-
-    filename = args[0]
-
-    with open(filename) as fh:
-        params = json.load(fh)
-    target_directory = params['output_data'][0]['extra_files_path']
-    os.mkdir(target_directory)
-    data_manager_dict = {}
-
-    dbkey = options.fasta_dbkey
-
-    if dbkey in [None, '', '?']:
-        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
-
-    sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
-
-    # build the index
-    build_bwa_index(
-        data_manager_dict,
-        options.fasta_filename,
-        params,
-        target_directory,
-        dbkey,
-        sequence_id,
-        sequence_name,
-        data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME
-    )
-
-    # save info to json file
-    with open(filename, 'w') as fh:
-        json.dump(data_manager_dict, fh, sort_keys=True)
-
-
-if __name__ == "__main__":
-    main()
diff -r 0429479e3821 -r 74dbe9e6c888 data_manager/bwa_mem_index_builder.xml
--- a/data_manager/bwa_mem_index_builder.xml	Sun Apr 16 08:27:00 2023 +0000
+++ b/data_manager/bwa_mem_index_builder.xml	Thu Dec 05 06:47:18 2024 +0000
@@ -1,17 +1,42 @@
-<tool id="bwa_mem_index_builder_data_manager" name="BWA-MEM index" tool_type="manage_data" version="0.0.5" profile="19.05">
+<tool id="bwa_mem_index_builder_data_manager" name="BWA-MEM index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>builder</description>
+    <macros>
+        <token name="@WRAPPER_VERSION@">0.7.18</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="0.7.17">bwa</requirement>
-        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="@WRAPPER_VERSION@">bwa</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/bwa_mem_index_builder.py'
-        '${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 bwa_mem_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 index
+        #if $index_algorithm != 'automatic':
+            -a '$index_algorithm'
+        #end if
+            '${out_file.extra_files_path}/${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 $all_fasta_source.fields.name
+{
+  "data_tables":{
+    "bwa_mem_indexes":[
+      {
+        "value": "${value}",
+        "dbkey": "${all_fasta_source.fields.dbkey}",
+        "name": "${name}",
+        "path": "${fasta_file_name}"
+      }
+    ]
+  }
+}
+]]></configfile>
+    </configfiles>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta"/>
@@ -23,6 +48,7 @@
             <option value="automatic" selected="true">Guess automatically (2GB cut-off)</option>
             <option value="is">IS linear-time algorithm (for small genomes)</option>
             <option value="bwtsw">BWT-SW (for large genomes)</option>
+            <option value="rb2">RB2</option>
         </param>
     </inputs>
     <outputs>
@@ -31,7 +57,14 @@
     <tests>
         <test>
             <param name="all_fasta_source" value="phiX174"/>
-            <output name="out_file" value="bwa_mem_data_manager.json"/>
+            <output name="out_file" value="bwa_mem_data_manager.1.json"/>
+        </test>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <param name="sequence_name" value="Galeocerdo cuvier"/>
+            <param name="sequence_id" value="tigHai1"/>
+            <param name="index_algorithm" value="bwtsw"/>
+            <output name="out_file" file="bwa_mem_data_manager.2.json"/>
         </test>
     </tests>
     <help>
diff -r 0429479e3821 -r 74dbe9e6c888 data_manager_conf.xml
--- a/data_manager_conf.xml	Sun Apr 16 08:27:00 2023 +0000
+++ b/data_manager_conf.xml	Thu Dec 05 06:47:18 2024 +0000
@@ -1,6 +1,5 @@
 <?xml version="1.0"?>
 <data_managers>
-
     <data_manager tool_file="data_manager/bwa_mem_index_builder.xml" id="bwa_mem_index_builder">
         <data_table name="bwa_mem_indexes">
             <output>
@@ -10,13 +9,12 @@
                 <column name="path" output_ref="out_file" >
                     <move type="directory" relativize_symlinks="True">
                         <!-- <source>${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}/bwa_mem_index/${value}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/bwa_mem_index/v1/${value}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bwa_mem_index/${value}/${path}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bwa_mem_index/v1/${value}/${path}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
         </data_table>
     </data_manager>
-   
 </data_managers>
diff -r 0429479e3821 -r 74dbe9e6c888 test-data/all_fasta.loc
--- a/test-data/all_fasta.loc	Sun Apr 16 08:27:00 2023 +0000
+++ b/test-data/all_fasta.loc	Thu Dec 05 06:47:18 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 0429479e3821 -r 74dbe9e6c888 test-data/bwa_mem_data_manager.1.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_mem_data_manager.1.json	Thu Dec 05 06:47:18 2024 +0000
@@ -0,0 +1,12 @@
+{
+  "data_tables":{
+    "bwa_mem_indexes":[
+      {
+        "value": "phiX174",
+        "dbkey": "phiX174",
+        "name": "phiX 174",
+        "path": "phiX174.fasta"
+      }
+    ]
+  }
+}
diff -r 0429479e3821 -r 74dbe9e6c888 test-data/bwa_mem_data_manager.2.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_mem_data_manager.2.json	Thu Dec 05 06:47:18 2024 +0000
@@ -0,0 +1,12 @@
+{
+  "data_tables":{
+    "bwa_mem_indexes":[
+      {
+        "value": "tigHai1",
+        "dbkey": "phiX174",
+        "name": "Galeocerdo cuvier",
+        "path": "phiX174.fasta"
+      }
+    ]
+  }
+}
diff -r 0429479e3821 -r 74dbe9e6c888 test-data/bwa_mem_data_manager.json
--- a/test-data/bwa_mem_data_manager.json	Sun Apr 16 08:27:00 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"data_tables": {"bwa_mem_indexes": [{"dbkey": "phiX174", "name": "phiX174", "path": "phiX174.fasta", "value": "phiX174"}]}}
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