Mercurial > repos > iuc > data_manager_hisat2_index_builder
changeset 8:e4f36467bb51 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit e5971e34b23280f7c3d6291a03325b6dd47e3fdd
| author | iuc |
|---|---|
| date | Sat, 16 Aug 2025 14:36:15 +0000 |
| parents | d74c740bdb25 |
| children | |
| files | data_manager/hisat2_index_builder.py data_manager/hisat2_index_builder.xml data_manager_conf.xml test-data/hisat2_data_manager.1.json test-data/hisat2_data_manager.2.json test-data/hisat2_data_manager.json |
| diffstat | 6 files changed, 81 insertions(+), 105 deletions(-) [+] |
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--- a/data_manager/hisat2_index_builder.py Sun Apr 16 08:30:13 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -#!/usr/bin/env python -# Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg -from __future__ import print_function - -import argparse -import json -import os -import shlex -import subprocess -import sys - -DEFAULT_DATA_TABLE_NAME = "hisat2_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_hisat_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) - fasta_base_name = os.path.split(options.fasta_filename)[-1] - sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name) - os.symlink(options.fasta_filename, sym_linked_fasta_filename) - args = ['hisat2-build'] - args.extend(shlex.split(options.indexer_options)) - args.extend([sym_linked_fasta_filename, sequence_id]) - 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=options.fasta_dbkey, name=sequence_name, path=sequence_id) - _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='hisat2_indexes') - parser.add_argument('--indexer_options', dest='indexer_options', action='store', type=str, default='') - 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_hisat_index(data_manager_dict, options, params, sequence_id, sequence_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()
--- a/data_manager/hisat2_index_builder.xml Sun Apr 16 08:30:13 2023 +0000 +++ b/data_manager/hisat2_index_builder.xml Sat Aug 16 14:36:15 2025 +0000 @@ -1,9 +1,15 @@ -<tool id="hisat2_index_builder_data_manager" name="HISAT2 index" tool_type="manage_data" version="2.1.0" profile="19.05"> +<tool id="hisat2_index_builder_data_manager" name="HISAT2 index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> <description>builder</description> + <macros> + <token name="@WRAPPER_VERSION@">2.2.1</token> + <token name="@VERSION_SUFFIX@">1</token> + </macros> <requirements> - <requirement type="package" version="2.1.0">hisat2</requirement> + <requirement type="package" version="@WRAPPER_VERSION@">hisat2</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + #set $value = $sequence_id or $all_fasta_source.fields.dbkey + #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] #if $advanced.adv_param_select == 'yes' and $advanced.gtf_input: ln -s '${advanced.gtf_input}' gtf_file.gtf && hisat2_extract_splice_sites.py gtf_file.gtf > splice_sites.txt && @@ -17,30 +23,53 @@ hisat2_extract_snps_haplotypes_UCSC.py '${all_fasta_source.fields.path}' snps.tabular extracted && #end if #end if - python '$__tool_directory__/hisat2_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}' - --data_table_name hisat2_indexes - --indexer_options "-p \${GALAXY_SLOTS:-1} + + mkdir -p '${out_file.extra_files_path}' && + ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' && + working="\$(pwd)" && + cd '${out_file.extra_files_path}' && + + hisat2-build -p "\${GALAXY_SLOTS:-1}" #if $advanced.adv_param_select == 'yes': --noauto #if $advanced.snps: - --snps "`pwd`/extracted.snp" - --haplotype "`pwd`/extracted.haplotype" + --snp "\${working}/extracted.snp" + --haplotype "\${working}/extracted.haplotype" #end if #if $advanced.gtf_input: - --ss "`pwd`/splice_sites.txt" - --exon "`pwd`/exon.txt" + --ss "\${working}/splice_sites.txt" + --exon "\${working}/exon.txt" #end if --bmax $advanced.bmax --bmaxdivn $advanced.bmaxdivn --dcv $advanced.dcv --offrate $advanced.offrate #end if - " + '${fasta_file_name}' '${value}' && + rm '${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 $all_fasta_source.fields.name +{ + "data_tables":{ + "hisat2_indexes":[ + { + "value": "${value}", + "dbkey": "${all_fasta_source.fields.dbkey}", + "name": "${name}", + "path": "${value}" + } + ] + } +} +]]></configfile> + </configfiles> <inputs> <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> <options from_data_table="all_fasta" /> @@ -69,7 +98,18 @@ <tests> <test> <param name="all_fasta_source" value="phiX174"/> - <output name="out_file" file="hisat2_data_manager.json"/> + <output name="out_file" file="hisat2_data_manager.1.json"/> + </test> + <test> + <param name="all_fasta_source" value="phiX174"/> + <param name="sequence_name" value="Galeocerdo cuvier"/> + <param name="sequence_id" value="tigHai1"/> + <param name="advanced|adv_param_select" value="yes"/> + <param name="advanced|bmax" value="3"/> + <param name="advanced|bmaxdivn" value="3"/> + <param name="advanced|dcv" value="4"/> + <param name="advanced|offrate" value="5"/> + <output name="out_file" file="hisat2_data_manager.2.json"/> </test> </tests> <help>
--- a/data_manager_conf.xml Sun Apr 16 08:30:13 2023 +0000 +++ b/data_manager_conf.xml Sat Aug 16 14:36:15 2025 +0000 @@ -9,12 +9,12 @@ <column name="path" output_ref="out_file" > <move type="directory" relativize_symlinks="True"> <!-- <source>${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}/hisat2_index/${value}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/hisat_index/v2/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/hisat2_index/${value}/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/hisat_index/v2/${value}/${value}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> </data_table> </data_manager> -</data_managers> \ No newline at end of file +</data_managers>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hisat2_data_manager.1.json Sat Aug 16 14:36:15 2025 +0000 @@ -0,0 +1,12 @@ +{ + "data_tables":{ + "hisat2_indexes":[ + { + "value": "phiX174", + "dbkey": "phiX174", + "name": "phiX174", + "path": "phiX174" + } + ] + } +}