Mercurial > repos > artbio > guppy_basecaller
changeset 0:fb42dde97559 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
| author | artbio |
|---|---|
| date | Wed, 18 Nov 2020 23:26:35 +0000 |
| parents | |
| children | 93b6cbff5ea4 |
| files | guppy_basecaller.xml |
| diffstat | 1 files changed, 274 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/guppy_basecaller.xml Wed Nov 18 23:26:35 2020 +0000 @@ -0,0 +1,274 @@ +<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.4" python_template_version="3.5"> + <description>A simple wrapper for guppy basecaller that depends on configuration files</description> + <requirements> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + #for $file in $infiles: + ln -s $file ${file.element_identifier}.fast5 && + #end for + tar xf $config && + guppy_basecaller -i . + --save_path out + --data_path . + --config *.cfg + --num_callers 4 + --records_per_fastq 0 + --cpu_threads_per_caller \${GALAXY_SLOTS:-2} + --disable_pings + --qscore_filtering + --calib_detect + ]]></command> + <inputs> + <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/> + <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/> + </inputs> + <outputs> + <data name="guppy_result" format="fastq"> + <discover_datasets directory="out/PASS" ext="fastq" pattern=".+\.fastq" visible="true"/> + </data> + </outputs> + <help><![CDATA[ + A wrapper for guppy basecaller. This expects two type of inputs: a collection of fast5 files, + and a configuration in the form of a tar file. + + You can find configurations at https://github.com/nanoporetech/rerio, + and in particular the directory https://github.com/nanoporetech/rerio/basecall_models. + + Each file there contains a URL you can download to use, for example + https://github.com/nanoporetech/rerio/blob/master/basecall_models/res_rna2_r941_min_flipflop_v001 + points to 'https://nanoporetech.box.com/shared/static/84e1jeudx8lr8ay7e9u1ebnvx3bk2kjf.tgz' + + When uploading these .tgz files take care to set the format to 'tar' (galaxy doesn't autodetect this?). + + The results should be fastq files. + +------ + +guppy_basecaller --help +: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 3.6.1+249406c, client-server API version 1.1.0 + +**Usage**:: + +With config file:: + + guppy_basecaller -i <input path> -s <save path> -c <config file> [options] + +With flowcell and kit name:: + + guppy_basecaller -i <input path> -s <save path> --flowcell <flowcell name> + --kit <kit name> + +List supported flowcells and kits:: + + guppy_basecaller --print_workflows + +Use server for basecalling:: + + guppy_basecaller -i <input path> -s <save path> -c <config file> + --port <server address> [options] + + +**Command line parameters**:: + + --trim_threshold arg Threshold above which data will be trimmed + (in standard deviations of current level + distribution). + --trim_min_events arg Adapter trimmer minimum stride intervals + after stall that must be seen. + --max_search_len arg Maximum number of samples to search through + for the stall + --override_scaling Manually provide scaling parameters rather + than estimating them from each read. + --scaling_med arg Median current value to use for manual + scaling. + --scaling_mad arg Median absolute deviation to use for manual + scaling. + --trim_strategy arg Trimming strategy to apply: 'dna' or 'rna' + (or 'none' to disable trimming) + --dmean_win_size arg Window size for coarse stall event + detection + --dmean_threshold arg Threhold for coarse stall event detection + --jump_threshold arg Threshold level for rna stall detection + --pt_scaling Enable polyT/adapter max detection for read + scaling. + --pt_median_offset arg Set polyT median offset for setting read + scaling median (default 2.5) + --adapter_pt_range_scale arg Set polyT/adapter range scale for setting + read scaling median absolute deviation + (default 5.2) + --pt_required_adapter_drop arg Set minimum required current drop from + adapter max to polyT detection. (default + 30.0) + --pt_minimum_read_start_index arg Set minimum index for read start sample + required to attempt polyT scaling. (default + 30) + --as_model_file arg Path to JSON model file for adapter + scaling. + --as_gpu_runners_per_device arg Number of runners per GPU device for + adapter scaling. + --as_cpu_threads_per_scaler arg Number of CPU worker threads per adapter + scaler + --as_reads_per_runner arg Maximum reads per runner for adapter + scaling. + --as_num_scalers arg Number of parallel scalers for adapter + scaling. + -m [ --model_file ] arg Path to JSON model file. + -k [ --kernel_path ] arg Path to GPU kernel files location (only + needed if builtin_scripts is false). + -x [ --device ] arg Specify basecalling device: 'auto', or + 'cuda:<device_id>'. + --builtin_scripts arg Whether to use GPU kernels that were + included at compile-time. + --chunk_size arg Stride intervals per chunk. + --chunks_per_runner arg Maximum chunks per runner. + --chunks_per_caller arg Soft limit on number of chunks in each + caller's queue. New reads will not be + queued while this is exceeded. + --high_priority_threshold arg Number of high priority chunks to process + for each medium priority chunk. + --medium_priority_threshold arg Number of medium priority chunks to process + for each low priority chunk. + --overlap arg Overlap between chunks (in stride + intervals). + --gpu_runners_per_device arg Number of runners per GPU device. + --cpu_threads_per_caller arg Number of CPU worker threads per + basecaller. + --num_callers arg Number of parallel basecallers to create. + --post_out Return full posterior matrix in output + fast5 file and/or called read message from + server. + --stay_penalty arg Scaling factor to apply to stay probability + calculation during transducer decode. + --qscore_offset arg Qscore calibration offset. + --qscore_scale arg Qscore calibration scale factor. + --temp_weight arg Temperature adjustment for weight matrix in + softmax layer of RNN. + --temp_bias arg Temperature adjustment for bias vector in + softmax layer of RNN. + --qscore_filtering Enable filtering of reads into PASS/FAIL + folders based on min qscore. + --min_qscore arg Minimum acceptable qscore for a read to be + filtered into the PASS folder + --reverse_sequence arg Reverse the called sequence (for RNA + sequencing). + --u_substitution arg Substitute 'U' for 'T' in the called + sequence (for RNA sequencing). + --log_speed_frequency arg How often to print out basecalling speed. + --barcode_kits arg Space separated list of barcoding kit(s) or + expansion kit(s) to detect against. Must be + in double quotes. + --trim_barcodes Trim the barcodes from the output sequences + in the FastQ files. + --num_extra_bases_trim arg How vigorous to be in trimming the barcode. + Default is 0 i.e. the length of the + detected barcode. A positive integer means + extra bases will be trimmed, a negative + number is how many fewer bases (less + vigorous) will be trimmed. + --arrangements_files arg Files containing arrangements. + --score_matrix_filename arg File containing mismatch score matrix. + --start_gap1 arg Gap penalty for aligning before the + reference. + --end_gap1 arg Gap penalty for aligning after the + reference. + --open_gap1 arg Penalty for opening a new gap in the + reference. + --extend_gap1 arg Penalty for extending a gap in the + reference. + --start_gap2 arg Gap penalty for aligning before the query. + --end_gap2 arg Gap penalty for aligning after the query. + --open_gap2 arg Penalty for opening a new gap in the query. + --extend_gap2 arg Penalty for extending a gap in the query. + --min_score arg Minimum score to consider a valid + alignment. + --min_score_rear_override arg Minimum score to consider a valid alignment + for the rear barcode only (and min_score + will then be used for the front only when + this is set). + --front_window_size arg Window size for the beginning barcode. + --rear_window_size arg Window size for the ending barcode. + --require_barcodes_both_ends Reads will only be classified if there is a + barcode above the min_score at both ends of + the read. + --allow_inferior_barcodes Reads will still be classified even if both + the barcodes at the front and rear (if + applicable) were not the best scoring + barcodes above the min_score. + --detect_mid_strand_barcodes Search for barcodes through the entire + length of the read. + --min_score_mid_barcodes arg Minimum score for a barcode to be detected + in the middle of a read. + --num_barcoding_buffers arg Number of GPU memory buffers to allocate to + perform barcoding into. Controls level of + parallelism on GPU for barcoding. + --num_barcode_threads arg Number of worker threads to use for + barcoding. + --calib_detect Enable calibration strand detection and + filtering. + --calib_reference arg Reference FASTA file containing calibration + strand. + --calib_min_sequence_length arg Minimum sequence length for reads to be + considered candidate calibration strands. + --calib_max_sequence_length arg Maximum sequence length for reads to be + considered candidate calibration strands. + --calib_min_coverage arg Minimum reference coverage to pass + calibration strand detection. + --print_workflows Output available workflows. + --flowcell arg Flowcell to find a configuration for + --kit arg Kit to find a configuration for + -z [ --quiet ] Quiet mode. Nothing will be output to + STDOUT if this option is set. + --trace_categories_logs arg Enable trace logs - list of strings with + the desired names. + --verbose_logs Enable verbose logs. + --disable_pings Disable the transmission of telemetry + pings. + --ping_url arg URL to send pings to + --ping_segment_duration arg Duration in minutes of each ping segment. + -q [ --records_per_fastq ] arg Maximum number of records per fastq file, 0 + means use a single file (per worker, per + run id). + --read_batch_size arg Maximum batch size, in reads, for grouping + input files. + --compress_fastq Compress fastq output files with gzip. + -i [ --input_path ] arg Path to input fast5 files. + --input_file_list arg Optional file containing list of input + fast5 files to process from the input_path. + -s [ --save_path ] arg Path to save fastq files. + -l [ --read_id_list ] arg File containing list of read ids to filter + to + -r [ --recursive ] Search for input files recursively. + --fast5_out Choice of whether to do fast5 output. + --resume Resume a previous basecall run using the + same output folder. + --progress_stats_frequency arg Frequency in seconds in which to report + progress statistics, if supplied will + replace the default progress display. + --max_block_size arg Maximum block size (in events) of basecall + messages to server. + -p [ --port ] arg Port for basecalling service. + --barcoding_config_file arg Configuration file to use for barcoding. + --num_barcode_threads arg Number of worker threads to use for + barcoding. + --disable_events Disable the transmission of event tables + when receiving reads back from the basecall + server. + --client_id arg Optional unique identifier (non-negative + integer) for this instance of the Guppy + Client Basecaller, if supplied will form + part of the output filenames. + --nested_output_folder If flagged output fastq files will be + written to a nested folder structure, based + on: protocol_group/sample/protocol/qscore_p + ass_fail/barcode_arrangement/ + -h [ --help ] produce help message + -v [ --version ] print version number + -c [ --config ] arg Config file to use + -d [ --data_path ] arg Path to use for loading any data files the + application requires. + + +------ + ]]></help> +</tool>