# HG changeset patch
# User iuc
# Date 1760645504 0
# Node ID 4d92281e3b304e078cbfcdd5fc730d9e1ccf2143
# Parent  566207ae614c71d64b805d344ee97ad8bfcc8eef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696

diff -r 566207ae614c -r 4d92281e3b30 data_manager/salmon_index_builder.py
--- a/data_manager/salmon_index_builder.py	Sun Apr 16 08:31:17 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-#!/usr/bin/env python
-# Based heavily on the kallisto data manager wrapper script by iuc
-from __future__ import print_function
-
-import argparse
-import json
-import os
-import subprocess
-import sys
-
-DEFAULT_DATA_TABLE_NAME = "salmon_indexes_versioned"
-
-
-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_salmon_index(data_manager_dict, options, params, sequence_id, sequence_name):
-    data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
-    target_directory = params['output_data'][0]['extra_files_path']
-    if not os.path.exists(target_directory):
-        os.mkdir(target_directory)
-    args = ['salmon', 'index']
-    if options.kmer_size != '':
-        args.append('-k')
-        args.append(options.kmer_size)
-    args.extend(['-t', options.fasta_filename, '-i', target_directory])
-    return_code = subprocess.call(args=args, shell=False)
-    if return_code:
-        print("Error building index.", file=sys.stderr)
-        sys.exit(return_code)
-    data_table_entry = dict(value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id, version=options.index_version)
-    _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():
-    # Parse Command Line
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--output', dest='output', action='store', type=str, default=None)
-    parser.add_argument('--fasta_filename', dest='fasta_filename', action='store', type=str, default=None)
-    parser.add_argument('--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None)
-    parser.add_argument('--fasta_description', dest='fasta_description', action='store', type=str, default=None)
-    parser.add_argument('--data_table_name', dest='data_table_name', action='store', type=str, default='salmon_indexes')
-    parser.add_argument('-v', '--index_version', dest='index_version', action='store', type=str, help='Use IndexVersion attribute from header.json')
-    parser.add_argument('-k', '--kmer_size', dest='kmer_size', action='store', type=str, help='kmer_size')
-    options = parser.parse_args()
-
-    filename = options.output
-
-    with open(filename) as fh:
-        params = json.load(fh)
-    data_manager_dict = {}
-
-    if options.fasta_dbkey in [None, '', '?']:
-        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % options.fasta_dbkey)
-
-    sequence_id, sequence_name = get_id_name(params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description)
-    # build the index
-    build_salmon_index(data_manager_dict, options, params, sequence_id, sequence_name)
-
-    # save info to json file
-    with open(filename, 'w') as out:
-        json.dump(data_manager_dict, out, sort_keys=True)
-
-
-if __name__ == "__main__":
-    main()
diff -r 566207ae614c -r 4d92281e3b30 data_manager/salmon_index_builder.xml
--- a/data_manager/salmon_index_builder.xml	Sun Apr 16 08:31:17 2023 +0000
+++ b/data_manager/salmon_index_builder.xml	Thu Oct 16 20:11:44 2025 +0000
@@ -1,42 +1,108 @@
-<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="1.3.0" profile="19.01">
+<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
     <description>index builder</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.3.0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@PROFILE@">24.0</token>
+        <token name="@IDX_VERSION@">q7</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.3.0">salmon</requirement>
-        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
     </requirements>
-   <macros>
-       <token name="@IDX_VERSION@">q7</token>
-   </macros>
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}'
-            --fasta_filename '${all_fasta_source.fields.path}'
-            --fasta_dbkey '${all_fasta_source.fields.dbkey}'
-            --fasta_description '${all_fasta_source.fields.name}'
-            --kmer_size "${kmer_size}"
-            --data_table_name salmon_indexes_versioned
-            --index_version @IDX_VERSION@
-        ]]>
-    </command>
+        ## https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
+        ## https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
+        
+        #for $transcripts in $transcriptome.fields.path.split(",")
+            (zcat '$transcripts' 2>/dev/null || cat '$transcripts') >> gentrome.fa &&
+        #end for
+        (zcat '$all_fasta_source.fields.path' 2>/dev/null || cat '$all_fasta_source.fields.path') >> gentrome.fa &&
+
+        (zcat '$all_fasta_source.fields.path' 2>/dev/null || cat '$all_fasta_source.fields.path') | awk '{if($1 ~ /^>/) print $1}' | cut -c2- | tr -d " " > decoys.txt &&
+
+        mkdir '$out_file.extra_files_path' &&
+
+        salmon index
+            -k $kmer_size
+            -t gentrome.fa
+            -d decoys.txt
+            -i '$out_file.extra_files_path'
+            -p "\${GALAXY_SLOTS:-12}"
+            $gencode
+            &&
+
+        cp '$dmjson' '$out_file'
+    ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[{
+#if str($sequence_id).strip() == ""
+    #set sequence_id = $all_fasta_source.fields.dbkey
+#end if
+#if str($sequence_name).strip() == ""
+    #set sequence_name = $all_fasta_source.fields.dbkey
+#end if
+
+  "data_tables":{
+    "salmon_indexes_versioned":[
+      {
+        "value": "$sequence_id",
+        "dbkey": "$all_fasta_source.fields.dbkey",
+        "name": "$sequence_name",
+        "path": "$out_file.extra_files_path",
+        "version": "@IDX_VERSION@"
+      }
+    ]
+  }
+}]]></configfile>
+    </configfiles>
     <inputs>
-        <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
+        <param label="Transcriptome sequences" name="transcriptome" optional="false" type="select">
+            <options from_data_table="transcriptomes" />
+        </param>
+        <param label="Genome" name="all_fasta_source" optional="false" type="select">
             <options from_data_table="all_fasta" />
         </param>
         <param name="sequence_name" type="text" value="" label="Name of sequence" />
         <param name="sequence_id" type="text" value="" label="ID for sequence" />
-        <param name="kmer_size" type="integer" optional='true' value="21" max="32" label="The size of the k-mer on which the index is built"
-                    help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be.  We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE "/>
+        <param name="kmer_size" type="integer" optional='true' value="31" max="32" label="The size of the k-mer on which the index is built"
+                    help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be.  We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE ">
+            <validator type="expression" message="Only odd values">value % 2 == 1</validator>
+        </param>
+        <param name="gencode" type="boolean" label="Transcript sequences are in gencode format" truevalue="--gencode" falsevalue="" checked="false" help="Will split  the transcript name at the first '|' character. These reduced names will be used in the output  and when looking for these transcripts in a gene to transcript GTF."/>
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json" />
     </outputs>
     <tests>
         <test>
+            <param name="transcriptome" value="phiX174"/>
             <param name="all_fasta_source" value="phiX174"/>
             <param name="sequence_name" value="sequence_name"/>
             <param name="sequence_id" value="sequence_id"/>
             <output name="out_file">
                 <assert_contents>
-                    <has_line line='{"data_tables": {"salmon_indexes_versioned": [{"dbkey": "phiX174", "name": "sequence_name", "path": "sequence_id", "value": "sequence_id", "version": "q7"}]}}' />
+                    <has_text text='"salmon_indexes_versioned"' />
+                    <has_text text='"dbkey": "phiX174"' />
+                    <has_text text='"name": "sequence_name"' />
+                    <has_text text='"value": "sequence_id"' />
+                    <has_text text='"version": "q7"' />
+                    <has_text text='"path":' />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="transcriptome" value="phiX174"/>
+            <param name="all_fasta_source" value="phiX174"/>
+            <param name="sequence_name" value=""/>
+            <param name="sequence_id" value=""/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"salmon_indexes_versioned"' />
+                    <has_text text='"dbkey": "phiX174"' />
+                    <has_text text='"name": "phiX174"' />
+                    <has_text text='"value": "phiX174"' />
+                    <has_text text='"version": "q7"' />
+                    <has_text text='"path":' />
                 </assert_contents>
             </output>
         </test>
@@ -45,7 +111,11 @@
 <![CDATA[
 .. class:: infomark
 
-**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+Indices are constructed as described here: https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
+        
+See also https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
+
+**Notice:** If you leave name, description, or id blank, it the dbkey of the genome will be used.
 ]]>
     </help>
     <citations>
diff -r 566207ae614c -r 4d92281e3b30 test-data/phiX174_transcripts.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174_transcripts.fasta	Thu Oct 16 20:11:44 2025 +0000
@@ -0,0 +1,118 @@
+>lcl|NC_001422.1_cds_NP_040703.1_1 [locus_tag=phiX174p01] [db_xref=GeneID:2546398] [protein=DNA replication initiation] [protein_id=NP_040703.1] [location=join(3981..5386,1..136)] [gbkey=CDS]
+ATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA
+AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGAT
+GGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGT
+GATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGT
+TAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCG
+CCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCT
+GCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT
+GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGC
+AATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTA
+GAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTG
+CCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTAC
+AGCTAATGGCCGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCT
+AATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA
+GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGC
+TAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAA
+AAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGC
+TGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT
+GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAG
+ATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGG
+CGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAA
+CCTGCAGAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAAT
+TATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAAT
+GA
+>lcl|NC_001422.1_cds_NP_040704.1_2 [locus_tag=phiX174p02] [db_xref=GeneID:2546406] [protein=DNA replication initiation] [protein_id=NP_040704.1] [location=join(4497..5386,1..136)] [gbkey=CDS]
+ATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTT
+GGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGC
+TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCA
+CACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATG
+CGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCG
+CCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACG
+CAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCA
+GTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAA
+AGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTC
+AGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAA
+TCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGA
+GATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTG
+CTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTTATCGCTTCCATGA
+CGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTAC
+TGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGA
+>lcl|NC_001422.1_cds_NP_040705.1_3 [locus_tag=phiX174p03] [db_xref=GeneID:2546405] [protein=head morphogenesis] [protein_id=NP_040705.1] [location=join(5075..5386,1..51)] [gbkey=CDS]
+ATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGC
+AACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG
+GTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGG
+AAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCT
+TCGATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTT
+CGGATATTTCTGA
+>lcl|NC_001422.1_cds_NP_040706.1_4 [locus_tag=phiX174p04] [db_xref=GeneID:2546403] [protein=K] [protein_id=NP_040706.1] [location=51..221] [gbkey=CDS]
+ATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC
+TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTC
+GCCATCAACTAACGATTCTGTCAAAAACTGA
+>lcl|NC_001422.1_cds_NP_040707.1_5 [locus_tag=phiX174p05] [db_xref=GeneID:2546402] [protein=terminase] [protein_id=NP_040707.1] [location=133..393] [gbkey=CDS]
+ATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAA
+CGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGA
+CTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGA
+TTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGA
+>lcl|NC_001422.1_cds_NP_040708.1_6 [locus_tag=phiX174p07] [db_xref=GeneID:2546399] [protein=head morphogenesis] [protein_id=NP_040708.1] [location=390..848] [gbkey=CDS]
+ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTT
+CTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGA
+CCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGC
+TTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGG
+CCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGC
+CGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA
+AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA
+>lcl|NC_001422.1_cds_NP_040709.1_7 [locus_tag=phiX174p08] [db_xref=GeneID:2546400] [protein=endolysin] [protein_id=NP_040709.1] [location=568..843] [gbkey=CDS]
+ATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGC
+TTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAAC
+ATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAG
+GAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAGTGA
+>lcl|NC_001422.1_cds_NP_040710.1_8 [locus_tag=phiX174p09] [db_xref=GeneID:2546404] [protein=DNA condensation] [protein_id=NP_040710.1] [location=848..964] [gbkey=CDS]
+ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA
+AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA
+>lcl|NC_001422.1_cds_NP_040711.1_9 [locus_tag=phiX174p06] [db_xref=GeneID:2546408] [protein=major head protein] [protein_id=NP_040711.1] [location=1001..2284] [gbkey=CDS]
+ATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC
+AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGT
+TGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTT
+TATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTC
+CTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATAC
+CAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGG
+ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCT
+GCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTC
+TACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGAT
+TACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC
+GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTC
+GTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG
+CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTA
+ACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCG
+TGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAG
+TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG
+AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTC
+CGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT
+CGCGATTCAATCATGACTTCGTGA
+>lcl|NC_001422.1_cds_NP_040712.1_10 [locus_tag=phiX174p06] [db_xref=GeneID:2546408] [protein=major spike protein] [protein_id=NP_040712.1] [location=2395..2922] [gbkey=CDS]
+ATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTA
+CTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTT
+GACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAAT
+CAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCT
+TTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGA
+TGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAACGTT
+TATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGG
+TTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGA
+>lcl|NC_001422.1_cds_NP_040713.1_11 [locus_tag=phiX174p06] [db_xref=GeneID:2546408] [protein=pilot protein for DNA ejection] [protein_id=NP_040713.1] [location=2931..3917] [gbkey=CDS]
+ATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAG
+GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCAT
+GGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT
+TTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG
+CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATAC
+TCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCT
+GCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAG
+AGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAA
+TACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTT
+GCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA
+CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGC
+TGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCA
+AAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAG
+CTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAG
+GAAATAA
+
diff -r 566207ae614c -r 4d92281e3b30 test-data/transcriptomes.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transcriptomes.loc	Thu Oct 16 20:11:44 2025 +0000
@@ -0,0 +1,1 @@
+phiX174	phiX174	phiX174	${__HERE__}/phiX174_transcripts.fasta
\ No newline at end of file
diff -r 566207ae614c -r 4d92281e3b30 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sun Apr 16 08:31:17 2023 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Oct 16 20:11:44 2025 +0000
@@ -8,4 +8,8 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/all_fasta.loc" />
     </table>
+    <table name="transcriptomes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/transcriptomes.loc" />
+    </table>
 </tables>
diff -r 566207ae614c -r 4d92281e3b30 tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Sun Apr 16 08:31:17 2023 +0000
+++ b/tool_data_table_conf.xml.test	Thu Oct 16 20:11:44 2025 +0000
@@ -8,4 +8,8 @@
         <columns>value, dbkey, name, path</columns>
         <file path="${__HERE__}/test-data/all_fasta.loc" />
     </table>
+        <table name="transcriptomes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/transcriptomes.loc" />
+    </table>
 </tables>