Mercurial > repos > dfornika > data_manager_build_kma_index
changeset 0:5e00d9417f68 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kma_index/ commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85
| author | dfornika |
|---|---|
| date | Thu, 03 Oct 2019 00:30:29 -0400 |
| parents | |
| children | 5a64b8429b31 |
| files | data_manager/kma_build_index.py data_manager/kma_build_index.xml data_manager_conf.xml tool-data/kma_index.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 166 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kma_build_index.py Thu Oct 03 00:30:29 2019 -0400 @@ -0,0 +1,91 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import errno +import json +import os +import uuid +import subprocess + + +DATA_TABLE_NAME = "kma_index" + +def kma_build_index(kma_index_args, index_name, target_directory, data_table_name=DATA_TABLE_NAME): + + 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"]), + str(kma_index_args["fasta"]), + ] + + subprocess.check_call(['kma index'] + args, cwd=target_directory) + + data_table_entry = { + 'data_tables': { + data_table_name: [ + { + "value": uuid.uuid4(), + "name": index_name, + "path": "seq", + } + ] + } + } + + return data_table_entry + + +def main(args): + + data_manager_input = json.loads(open(args.data_manager_json).read()) + + 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, + ) + + open(args.data_manager_json, 'w').write(json.dumps(data_manager_output)) + + +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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kma_build_index.xml Thu Oct 03 00:30:29 2019 -0400 @@ -0,0 +1,49 @@ +<?xml version="1.0"?> +<tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.2.12+galaxy0"> + <description>kma index builder</description> + <requirements> + <requirement type="package" version="1.2.12">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} + ${fasta} + ]]> + </command> + <inputs> + <param name="k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." /> + <param name="k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." /> + <param name="k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." /> + <param name="ML" type="integer" value="16" label="Minimum length of templates" /> + <param name="ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" /> + <param name="hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" /> + <param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <help> + </help> + <citations> + <citation type="bibtex"> + @article{clausen2018rapid, + title={Rapid and precise alignment of raw reads against redundant databases with KMA}, + author={Clausen, Philip TLC and Aarestrup, Frank M and Lund, Ole}, + journal={BMC bioinformatics}, + volume={19}, + number={1}, + pages={307}, + year={2018}, + publisher={BioMed Central} + } + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Thu Oct 03 00:30:29 2019 -0400 @@ -0,0 +1,18 @@ +<data_managers> + <data_manager tool_file="data_manager/kma_build_index.xml" id="kma_build_index" version="0.1.0"> + <data_table name="kma_index"> + <output> + <column name="value"/> + <column name="name"/> + <column name="path" output_ref="out_file"> + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Oct 03 00:30:29 2019 -0400 @@ -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="tool-data/kma_index.loc" /> + </table> +</tables>