<commit_before>"""
Usage:
biobox run short_read_assembler <image> [--no-rm] --input=FILE --output=FILE [--task=TASK]

Options:
-h, --help              Show this screen.
-v, --version           Show version.
-i FILE, --input=FILE   Source FASTQ file containing paired short reads
-o FILE, --output=FILE  Destination FASTA file for assembled contigs
-t TASK, --task=TASK    Optionally specify a biobox task to run [default: default]
-r, --no-rm             Don't remove the container after the process finishes
"""

import biobox_cli.container   as ctn
import biobox_cli.biobox_file as fle
from biobox_cli.biobox import Biobox

import os

class Assembler(Biobox):

    def copy_contigs_file(self,biobox_output_dir, biobox_output, dst):
        contigs = biobox_output['arguments'][0]['fasta'][0]['value']
        src = os.path.join(biobox_output_dir, contigs)
        import shutil
        shutil.move(src, dst)<commit_msg>add usage space for tests<commit_after>"""
Usage:
    biobox run short_read_assembler <image> [--no-rm] --input=FILE --output=FILE [--task=TASK]

Options:
-h, --help              Show this screen.
-v, --version           Show version.
-i FILE, --input=FILE   Source FASTQ file containing paired short reads
-o FILE, --output=FILE  Destination FASTA file for assembled contigs
-t TASK, --task=TASK    Optionally specify a biobox task to run [default: default]
-r, --no-rm             Don't remove the container after the process finishes
"""

import biobox_cli.container   as ctn
import biobox_cli.biobox_file as fle
from biobox_cli.biobox import Biobox

import os

class Assembler(Biobox):

    def copy_contigs_file(self,biobox_output_dir, biobox_output, dst):
        contigs = biobox_output['arguments'][0]['fasta'][0]['value']
        src = os.path.join(biobox_output_dir, contigs)
        import shutil
        shutil.move(src, dst)
{'fraction_non_alphanumeric': 0.10979547900968784, 'fraction_numerical': 0.002152852529601722, 'mean_word_length': 3.2933025404157044, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5003426', 'n_tokens_mistral': 622, 'n_tokens_neox': 590, 'n_words': 183}