# HG changeset patch
# User iuc
# Date 1760097790 0
# Node ID b221a6c2ed001e602dfacd07b77865c14d4d195a
# Parent  2c532a6eee3f13d08a962ce23708720173d6893b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1

diff -r 2c532a6eee3f -r b221a6c2ed00 data_manager/kma_build_index.py
--- a/data_manager/kma_build_index.py	Sun Nov 22 12:45:39 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,97 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-
-import argparse
-import errno
-import json
-import os
-import subprocess
-import uuid
-
-
-DATA_TABLE_NAME = "kma_index"
-
-
-def kma_build_index(kma_index_args, index_name, target_directory, data_table_name=DATA_TABLE_NAME):
-    UUID = str(uuid.uuid4())
-
-    os.mkdir(os.path.join(target_directory, UUID))
-
-    args = [
-        '-k', str(kma_index_args["k"]),
-        '-k_t', str(kma_index_args["k_t"]),
-        '-k_i', str(kma_index_args["k_i"]),
-        '-ML', str(kma_index_args["ML"]),
-        '-ht', str(kma_index_args["ht"]),
-        '-hq', str(kma_index_args["hq"]),
-        '-o', os.path.join(UUID, "index"),
-        '-i', " ".join(kma_index_args["fasta"]),
-    ]
-
-    subprocess.check_call(' '.join(['kma index'] + args), cwd=target_directory, shell=True)
-
-    data_table_entry = {
-        'data_tables': {
-            data_table_name: [
-                {
-                    "value": UUID,
-                    "name": index_name,
-                    "path": os.path.join(UUID, "index"),
-                }
-            ]
-        }
-    }
-
-    return data_table_entry
-
-
-def main(args):
-    with open(args.data_manager_json) as fh:
-        data_manager_input = json.load(fh)
-
-    target_directory = data_manager_input['output_data'][0]['extra_files_path']
-
-    try:
-        os.mkdir(target_directory)
-    except OSError as exc:
-        if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
-            pass
-        else:
-            raise
-
-    data_manager_output = {}
-
-    kma_index_args = {
-        "k": args.k,
-        "k_t": args.k_t,
-        "k_i": args.k_i,
-        "ML": args.ML,
-        "ht": args.ht,
-        "hq": args.hq,
-        "fasta": args.fasta,
-    }
-
-    data_manager_output = kma_build_index(
-        kma_index_args,
-        args.index_name,
-        target_directory,
-    )
-
-    with open(args.data_manager_json, 'w') as fh:
-        json.dump(data_manager_output, fh, sort_keys=True)
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument('data_manager_json')
-    parser.add_argument('--k', dest='k', type=int, default=16, help='')
-    parser.add_argument('--k_t', dest='k_t', type=int, default=16, help='')
-    parser.add_argument('--k_i', dest='k_i', type=int, default=16, help='')
-    parser.add_argument('--ML', dest='ML', type=int, default=16, help='')
-    parser.add_argument('--ht', dest='ht', type=float, default=1.0, help='')
-    parser.add_argument('--hq', dest='hq', type=float, default=1.0, help='')
-    parser.add_argument('--name', dest='index_name', help='')
-    parser.add_argument('fasta', nargs='+', help='fasta file(s) to index')
-    args = parser.parse_args()
-    main(args)
diff -r 2c532a6eee3f -r b221a6c2ed00 data_manager/kma_build_index.xml
--- a/data_manager/kma_build_index.xml	Sun Nov 22 12:45:39 2020 +0000
+++ b/data_manager/kma_build_index.xml	Fri Oct 10 12:03:10 2025 +0000
@@ -1,47 +1,70 @@
 <?xml version="1.0"?>
-<tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.2.21+galaxy0" profile="19.01">
+<tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.6.6+galaxy0" profile="24.1">
     <description>kma index builder</description>
     <requirements>
-        <requirement type="package" version="1.2.21">kma</requirement>
-        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="1.6.6">kma</requirement>
     </requirements>
     <version_command>kma -v</version_command>
     <command detect_errors="exit_code">
     <![CDATA[
-        python '${__tool_directory__}/kma_build_index.py'
-          '${out_file}'
-          --k ${k}
-          --k_t ${k_t}
-          --k_i ${k_i}
-	  --ML ${ML}
-	  --ht ${ht}
-	  --hq ${hq}
-          --name '${name}'
-	  '${fasta}'
-    ]]>
-    </command>
+mkdir -p '${out_file.extra_files_path}'/index_folder &&
+kma_index
+  -i '$fasta'
+  -o '${out_file.extra_files_path}'/index_folder/index
+  ## index options
+  -k $k
+  -k_t $k_t
+  -k_i $k_i
+  -ML $ML
+  -ht $ht
+  -hq $hq
+    ]]></command>
+    <configfiles>
+        <configfile filename="dm.json"><![CDATA[#slurp
+#from datetime import datetime
+#from hashlib import md5
+#set value=datetime.now().strftime("%Y-%m-%d") + "_" + md5($name.encode()).hexdigest()
+{"data_tables": {"kma_index": [{"value": "$value", "name": "$name", "path": "index_folder"}]}}
+]]></configfile>
+    </configfiles>
     <inputs>
-        <param name="k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." />
-        <param name="k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." />
-        <param name="k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." />
-        <param name="ML" type="integer" value="16" label="Minimum length of templates" />
-        <param name="ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" />
-        <param name="hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" />
-	<param name="name" type="text" label="Name for index" />
-	<param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" />
+        <param argument="-k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." />
+        <param argument="-k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." />
+        <param argument="-k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." />
+        <param argument="-ML" type="integer" value="16" label="Minimum length of templates" />
+        <param argument="-ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" />
+        <param argument="-hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" />
+        <param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" />
+        <param name="name" type="text" optional="false" label="Name for index" help="Choose a name that describes the indexed sequence and possibly any non-default indexing parameters.">
+            <validator type="empty_field"/>
+        </param>
     </inputs>
     <outputs>
-        <data name="out_file" format="data_manager_json" />
+        <data name="out_file" format="data_manager_json" from_work_dir="dm.json"/>
     </outputs>
     <tests>
         <test>
             <param name="fasta" value="phiX174.fasta"/>
             <param name="name" value="index"/>
-            <output name="out_file" value="kma_data_manager.json" compare="sim_size" />
+            <output name="out_file" ftype="data_manager_json">
+                <assert_contents>
+                    <has_text text='"kma_index":' />
+                    <has_text text='"name": "index"' />
+                    <has_text text='"path": "index_folder"' />
+                    <has_text_matching expression='"value": "\d{4}-\d{2}-\d{2}_6a992d5529f459a44fee58c733255e86"' />
+                </assert_contents>
+            </output>
         </test>
     </tests>
-    <help>
-    </help>
+    <help><![CDATA[
+**Data manager for building an index for the kma aligner**
+
+Runs the kma index command on the input sequence with the chosen options.
+
+.. class:: infomark
+
+   You may want to capture details about the reference sequence and any non-default indexing parameters in the name of the index so that users have a better idea what they are selecting for tool runs.
+    ]]></help>
     <citations>
         <citation type="doi">10.1186/s12859-018-2336-6</citation>
     </citations>
diff -r 2c532a6eee3f -r b221a6c2ed00 data_manager_conf.xml
--- a/data_manager_conf.xml	Sun Nov 22 12:45:39 2020 +0000
+++ b/data_manager_conf.xml	Fri Oct 10 12:03:10 2025 +0000
@@ -6,10 +6,10 @@
 		<column name="name"/>
 		<column name="path" output_ref="out_file">
 		    <move type="directory">
-		        <source>#import os#${os.path.dirname($path)}</source>
-			<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kma_index/#import os#${os.path.dirname($path)}</target>
+		        <source>${path}</source>
+				<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kma_index/${value}</target>
 		    </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kma_index/${path}</value_translation>
+			<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kma_index/${value}/index</value_translation>
 		    <value_translation type="function">abspath</value_translation>
 		</column>
 	    </output>
diff -r 2c532a6eee3f -r b221a6c2ed00 test-data/kma_data_manager.json
--- a/test-data/kma_data_manager.json	Sun Nov 22 12:45:39 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"data_tables": {"kma_index": [{"name": "b153d490-f0f2-4980-8d1b-c7365e4d69ec/index", "path": "index", "value": "b153d490-f0f2-4980-8d1b-c7365e4d69ec"}]}}
diff -r 2c532a6eee3f -r b221a6c2ed00 test-data/kma_index.loc
diff -r 2c532a6eee3f -r b221a6c2ed00 tool-data/kma_index.loc.sample
--- a/tool-data/kma_index.loc.sample	Sun Nov 22 12:45:39 2020 +0000
+++ b/tool-data/kma_index.loc.sample	Fri Oct 10 12:03:10 2025 +0000
@@ -0,0 +1,8 @@
+# This data table has records in the format
+# value    name    path
+# where paths point to folders with kma index files but include the common prefix (always index) of these files.
+# A record could look like this:
+# 2025-10-10_abbf9e73ffdc7e46450db9781b23e605    an_example_index      /tool-data/kma_index/2025-10-10_abbf9e73ffdc7e46450db9781b23e605/index
+# with the following files inside /tool-data/kma_index/2025-10-10_abbf9e73ffdc7e46450db9781b23e605/:
+# index.comp.b  index.length.b  index.name  index.seq.b
+# The entire recorded path (including the /index) can be passed to kma unaltered and it will discover the index files from it.
diff -r 2c532a6eee3f -r b221a6c2ed00 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Oct 10 12:03:10 2025 +0000
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of kma indexes in the required format -->
+    <table name="kma_index" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/kma_index.loc" />
+    </table>
+</tables>